Monitoring Microbial Mineralization Using Reverse Stable Isotope Labeling Analysis by Mid-Infrared Laser Spectroscopy.
ABSTRACT: Assessing the biodegradation of organic compounds is a frequent question in environmental science. Here, we present a sensitive, inexpensive, and simple approach to monitor microbial mineralization using reverse stable isotope labeling analysis (RIL) of dissolved inorganic carbon (DIC). The medium for the biodegradation assay contains regular organic compounds and 13C-labeled DIC with 13C atom fractions (x(13C)DIC) higher than natural abundance (typically 2-50%). The produced CO2 (x(13C) ? 1.11%) gradually dilutes the initial x(13C)DIC allowing to quantify microbial mineralization using mass-balance calculations. For 13C-enriched CO2 samples, a newly developed isotope ratio mid-infrared spectrometer was introduced with a precision of x(13C) < 0.006%. As an example for extremely difficult and slowly degradable compounds, CO2 production was close to the theoretical stoichiometry for anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Furthermore, we could measure the aerobic degradation of dissolved organic carbon (DOC) adsorbed to granular activated carbon in a drinking water production plant, which cannot be labeled with 13C. Thus, the RIL approach can be applied to sensitively monitor biodegradation of various organic compounds under anoxic or oxic conditions.
Project description:Northern permafrost soils store a vast reservoir of carbon, nearly twice that of the present atmosphere. Current and projected climate warming threatens widespread thaw of these frozen, organic carbon (OC)-rich soils. Upon thaw, mobilized permafrost OC in dissolved and particulate forms can enter streams and rivers, which are important processors of OC and conduits for carbon dioxide (CO2) to the atmosphere. Here, we demonstrate that ancient dissolved organic carbon (DOC) leached from 35,800 y B.P. permafrost soils is rapidly mineralized to CO2. During 200-h experiments in a novel high-temporal-resolution bioreactor, DOC concentration decreased by an average of 53%, fueling a more than sevenfold increase in dissolved inorganic carbon (DIC) concentration. Eighty-seven percent of the DOC loss to microbial uptake was derived from the low-molecular-weight (LMW) organic acids acetate and butyrate. To our knowledge, our study is the first to directly quantify high CO2 production rates from permafrost-derived LMW DOC mineralization. The observed DOC loss rates are among the highest reported for permafrost carbon and demonstrate the potential importance of LMW DOC in driving the rapid metabolism of Pleistocene-age permafrost carbon upon thaw and the outgassing of CO2 to the atmosphere by soils and nearby inland waters.
Project description:Although the biological fixation of CO2 by chemolithoautotrophs provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs as a carbon and energy source, the relative amounts of autotrophic C in chemotrophic microbial communities are not well-established. The extent and mechanisms of CO2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous "streamer" communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeota and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum fractions of autotrophic C in microbial biomass were >50% in the majority of communities analyzed. The significance of CO2 as a C source in these communities provides a foundation for understanding community assembly and succession, and metabolic linkages among early-branching thermophilic autotrophs and heterotrophs.
Project description:Ten field cruises were carried out in Tagus estuary from 1999 to 2007 to study the dynamics of the inorganic carbon system. Dissolved inorganic carbon (DIC) and total alkalinity (TA) increased with salinity. DIC and TA were generally conservative in the estuarine mixing zone (salinity > 10), while a complex distribution pattern was observed at the upper estuary. DIC values peaked 1786.9 ± 155.8 µmol kg-1 at that segment. Estimated annual mean fluxes of DIC were 0.27 Tg C yr-1 from the river to the estuary, and 0.37 Tg C yr-1 from here to the coastal area. The Tagus estuary was always CO2 supersaturated, with partial pressure of CO2 (pCO2) reaching 9160 µatm in the upper estuary. An average emission of 0.11 Tg C yr-1 was estimated from the estuary to the atmosphere, corresponding to 23% of exported DIC. Only 8% of the riverine DIC was ventilated. The non-conservative behaviour of CO2 parameters in the estuary segment under freshwater influence was attributed to alternations in the relevance of riverine/terrestrial runoff, photosynthesis, aerobic respiration, organic matter mineralization and CaCO3 precipitation/dissolution.
Project description:The carbon isotopic composition (?13C) of dissolved and particulate inorganic carbon (DIC; PIC) was used to compare and analyze the origin, dynamics and evolution of inorganic carbon in two headwater tributaries of the Xi River, Southwest China. Carbonate dissolution and soil CO2 were regarded as the primary sources of DIC on the basis of ?13CDIC values which varied along the Nanpan and Beipan Rivers, from -13.9‰ to 8.1‰. Spatial trends in DIC differed between the two rivers (i.e., the tributaries), in part because factors controlling pCO2, which strongly affected carbonate dissolution, differed between the two river basins. Transport of soil CO2 and organic carbon through hydrologic conduits predominately controlled the levels of pCO2 in the Nanpan River. However, pCO2 along the upper reaches of the Nanpan River also was controlled by the extent of urbanization and industrialization relative to agriculture. DIC concentrations in the highly urbanized upper reaches of the Nanpan River were typical higher than in other carbonate-dominated areas of the upper Xi River. Within the Beipan River, the oxidation of organic carbon is the primary process that maintains pCO2 levels. The pCO2 within the Beipan River was more affected by sulfuric acid from coal industries, inputs from a scenic spot, and groundwater than along the Nanpan River. With regards to PIC, the contents and ?13C values in the Nanpan River were generally lower than those in the Beipan River, indicating that chemical and physical weathering contributes more marine carbonate detritus to the PIC along the Beipan River. The CO2 evasion flux from the Nanpan River was higher than that in the Beipan River, and generally higher than along the middle and lower reaches of the Xi River, demonstrating that the Nanpan River is an important net source of atmospheric CO2 in Southwest China.
Project description:Methyl substrates are important compounds for methanogenesis in marine sediments but diversity and carbon utilization by methylotrophic methanogenic archaea have not been clarified. Here, we demonstrate that RNA-stable isotope probing (SIP) requires 13C-labeled bicarbonate as co-substrate for identification of methylotrophic methanogens in sediment samples of the Helgoland mud area, North Sea. Using lipid-SIP, we found that methylotrophic methanogens incorporate 60-86% of dissolved inorganic carbon (DIC) into lipids, and thus considerably more than what can be predicted from known metabolic pathways (~40% contribution). In slurry experiments amended with the marine methylotroph Methanococcoides methylutens, up to 12% of methane was produced from CO2, indicating that CO2-dependent methanogenesis is an alternative methanogenic pathway and suggesting that obligate methylotrophic methanogens grow in fact mixotrophically on methyl compounds and DIC. Although methane formation from methanol is the primary pathway of methanogenesis, the observed high DIC incorporation into lipids is likely linked to CO2-dependent methanogenesis, which was triggered when methane production rates were low. Since methylotrophic methanogenesis rates are much lower in marine sediments than under optimal conditions in pure culture, CO2 conversion to methane is an important but previously overlooked methanogenic process in sediments for methylotrophic methanogens.
Project description:The fixation of inorganic carbon has been documented in all three domains of life and results in the biosynthesis of diverse organic compounds that support heterotrophic organisms. The primary aim of this study was to assess carbon dioxide fixation in high-temperature Fe(III)-oxide mat communities and in pure cultures of a dominant Fe(II)-oxidizing organism (Metallosphaera yellowstonensis strain MK1) originally isolated from these environments. Protein-encoding genes of the complete 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) carbon dioxide fixation pathway were identified in M. yellowstonensis strain MK1. Highly similar M. yellowstonensis genes for this pathway were identified in metagenomes of replicate Fe(III)-oxide mats, as were genes for the reductive tricarboxylic acid cycle from Hydrogenobaculum spp. (Aquificales). Stable-isotope ((13)CO2) labeling demonstrated CO2 fixation by M. yellowstonensis strain MK1 and in ex situ assays containing live Fe(III)-oxide microbial mats. The results showed that strain MK1 fixes CO2 with a fractionation factor of ?2.5‰. Analysis of the (13)C composition of dissolved inorganic C (DIC), dissolved organic C (DOC), landscape C, and microbial mat C showed that mat C is from both DIC and non-DIC sources. An isotopic mixing model showed that biomass C contains a minimum of 42% C of DIC origin, depending on the fraction of landscape C that is present. The significance of DIC as a major carbon source for Fe(III)-oxide mat communities provides a foundation for examining microbial interactions that are dependent on the activity of autotrophic organisms (i.e., Hydrogenobaculum and Metallosphaera spp.) in simplified natural communities.
Project description:The decomposition processes of accumulated cyanobacteria can release large amounts of organic carbon and affect the carbon cycling in shallow eutrophic lakes. However, the migration and transformation mechanisms of dissolved carbon (DC) require further study and discussion. In this study, a 73-day laboratory microcosm experiment using suction samplers (Rhizon and syringe) was conducted to understand the migration and transformation of DC during the cyanobacteria decomposition. The decomposition of cyanobacteria biomass caused anoxic and reduction conditions, and changed the acid-base environment in the water column. During the early incubation (days 0-18), a large amount of cyanobacteria-derived particulate organic matter (POM) was decomposed into dissolved organic carbon (DOC) in the overlying water, reaching the highest peak value of 1.82 g L-1 in the treatment added the high cyanobacteria biomass (470 g). After 18 days of incubation, the mineralization of increased DOC to dissolved inorganic carbon (DIC) maintained a high DIC level of overlying water in treatments added cyanobacteria biomass. The treatment added the medium cyanobacteria biomass (235 g) presented the lower DOC/total dissolved carbon ratio than the high cyanobacteria biomass associated with the lower mineralization from DOC to DIC. Due to the concentration differences of DIC at water-sediment interface, the main migration of DIC from pore water to overlying water occurred in the treatment without added cyanobacteria biomass. However, the treatments added the cyanobacteria biomass presented the obvious diffusion of DOC and the low migration of DIC at the water-sediment interface. The diffusive fluxes of DOC at the water-sediment interface increased with the cyanobacteria biomass added, reaching the maximum value of 411.01 mg/(m2·d) in the treatment added the high cyanobacteria biomass. In the overlying water, the group added the sediment and medium cyanobacteria biomass presented a faster degradation of cyanobacteria-derived POM to DOC and a higher mineralization level of DOC to DIC than added the medium cyanobacteria biomass without sediment. Therefore, during accumulated cyanobacteria decomposition, the biomass of accumulated cyanobacteria and sediment property can influence the migration and transformation of DC, playing an important role in carbon cycling in shallow eutrophic lakes.
Project description:It is well established that stream dissolved inorganic carbon (DIC) fluxes play a central role in the global C cycle, yet the sources of stream DIC remain to a large extent unresolved. Here, we explore large-scale patterns in ?13C-DIC from streams across Sweden to separate and further quantify the sources and sinks of stream DIC. We found that stream DIC is governed by a variety of sources and sinks including biogenic and geogenic sources, CO2 evasion, as well as in-stream processes. Although soil respiration was the main source of DIC across all streams, a geogenic DIC influence was identified in the northernmost region. All streams were affected by various degrees of atmospheric CO2 evasion, but residual variance in ?13C-DIC also indicated a significant influence of in-stream metabolism and anaerobic processes. Due to those multiple sources and sinks, we emphasize that simply quantifying aquatic DIC fluxes will not be sufficient to characterise their role in the global C cycle.
Project description:High-latitude soils store ~40% of the global soil carbon and experience winters of up to 6 months or more. The winter soil CO2 efflux importantly contributes to the annual CO2 budget. Microorganisms can metabolize short chain carbon compounds in frozen soils. However, soil organic matter (SOM) is dominated by biopolymers, requiring exoenzymatic hydrolysis prior to mineralization. For winter SOM decomposition to have a substantial influence on soil carbon balances it is crucial whether or not biopolymers can be metabolized in frozen soils. We added 13C-labeled cellulose to frozen (-4?°C) mesocosms of boreal forest soil and followed its decomposition. Here we show that cellulose biopolymers are hydrolyzed under frozen conditions sustaining both CO2 production and microbial growth contributing to slow, but persistent, SOM mineralization. Given the long periods with frozen soils at high latitudes these findings are essential for understanding the contribution from winter to the global carbon balance.
Project description:The chemical composition of the Gaoping River in Taiwan reflects the weathering of both silicate and carbonate rocks found in its metasedimentary catchment. Major dissolved ion chemistry and radiocarbon signatures of dissolved inorganic carbon (DIC) reveal the importance of pyrite-derived sulphuric acid weathering on silicates and carbonates. Two-thirds of the dissolved load of the Gaoping River derives from sulphuric acid-mediated weathering of rocks within its catchment. This is reflected in the lowest reported signatures DI14C for a small mountainous river (43 to 71 percent modern carbon), with rock-derived carbonate constituting a 14C-free DIC source. Using an inverse modelling approach integrating riverine major dissolved ion chemistry and DI14C, we provide quantitative constraints of mineral weathering pathways and calculate atmospheric CO2 fluxes resulting from the erosion of the Taiwan orogeny over geological timescales. The results reveal that weathering on Taiwan releases 0.31?±?0.12 MtC/yr, which is offset by burial of terrestrial biospheric organic carbon in offshore sediments. The latter tips the balance with respect to the total CO2 budget of Taiwan such that the overall system acts as a net sink, with 0.24?±?0.13 MtC/yr of atmospheric CO2 consumed over geological timescales.