Hydrogen turnover by psychrotrophic homoacetogenic and mesophilic methanogenic bacteria in anoxic paddy soil and lake sediment

Abstract The effect of temperature on CH₄ production, turnover of dissolved H₂, and enrichment of H₂-utilizing anaerobic bacteria was studied in anoxic paddy soil and sediment of Lake Constance. When anoxic paddy soil was incubated under an atmosphere of H₂/CO₂, rates of CH₄ production increased 25°C, but decreased at temperatures lower than 20°C. Chloroform completely inhibited methano-genesis in anoxic paddy soil and lake sediment, but did not or only partially inhibit the turnover of dissolved H₂, especially at low incubation temperatures. Cultures with H₂ as energy source resulted in the enrichment of chemolithotrophic homoacetogenic bacteria whenever incubation temperatures were lower than 20°C. Hydrogenotrophic methanogens could only be enriched at 30°C from anoxic paddy soil. A homoacetogen     

Production, oxidation and emission of methane in rice paddies

Abstract Production and emission of methane from submerged paddy soil was studied in laboratory rice cultures and in Italian paddy fields. Up to 80% of the CH₄ produced in the paddy soil did not reach the atmosphere but was apparently oxidized in the rhizosphere. CH₄ emission through the rice plants was inhibited by an atmosphere of pure O₂ but was stimulated by an atmosphere of pure N₂ or an atmosphere containing 5% acetylene. Gas bubbles taken from the submerged soil contained up to 60% CH₄, but only < 1% CH₄ after the bubbles had passed the soil-water interface or had entered the intercellular gas space system of the rice plants. CH₄ oxidation activities were detected in the oxic surface layer of the submerged paddy soil. Flooding the paddy soil with water containing > 0.15% sea salt (0.01% sulfate) resulted in a strong inhibition of the rates of methanogenesis and a decrease in the rates of CH₄ emission. This result explains the observation of relatively low CH₄ emission rates in rice paddy areas flooded with brackish water.     

Temporal change of gas metabolism by hydrogen-syntrophic methanogenic bacterial associations in anoxic paddy soil

Abstract Interspecies H₂ transfer within methanogenic bacterial associations (MBA) accounted for 95–97% of the conversion of ¹⁴CO₂ to ¹⁴CH₄ in anoxic paddy soil. Only 3–5% of the ¹⁴CH₄ were produced from the turnover of dissolved H₂. The H₂-syntrophic MBA developed within 5 days after the paddy soil had been submerged and placed under anoxic atmosphere. Afterwards, both the contribution of MBA to H₂-dependent methanogenesis and the turnover of dissolved H₂ did not change significantly for up to 7 months of incubation. However, while the rates of H₂-dependent methanogenesis stayed relatively constant, the rates of total methanogenesis decreased. The contribution of MBA to H₂-dependent methanogenesis was further enhanced to 99% when the temperature was shifted from 30°C to 17°C, or when the soil had been planted with rice. This enhancement was partially due to an increased utilization of dissolved H₂ by chloroform-insensitive non-methanogenic bacteria, most probably homoacetogens, so that CH₄ production was almost completely restricted to H₂-syntrophic MBA. The activity of MBA, as measured by the conversion of ¹⁴CO₂ to ¹⁴CH₄, was stimulated by glucose, lactate, and ethanol to a similar or greater extent than by exogenous H₂. Propionate and acetate had no effect.     

Sensitivity of methanogenic bacteria from paddy soil to oxygen and desiccation

Abstract The effects of combinations of desiccation and exposure to O₂ were studied in pure cultures of Methanosarcina barkeri strain Fusaro and in a new Methanosarcina strain and a new Methanobacterium strain which were both isolated from dry oxic paddy soil. Incubation of bacterial suspensions under air for 200 min resulted in a decreased potential to produce CH₄, but not in a decreased viability. The inhibitory effect of O₂ slightly increased with increased salt concentration. Desiccation of bacterial suspensions under N₂ resulted in reduction of viability to 10% and of potential CH₄ production to 0.6%. Desiccation of bacterial suspensions under air resulted in a larger decrease of both viability (0.5%) and potential CH₄ production (0.03%). This decrease was smaller at rapid compared to slow desiccation. Survival and potential CH₄ production were further inhibited when the suspension was dried in the presence of sand grains or glass beads coated with FeS or FeNH₄PO₄. However, survival and potential CH₄ production increased dramatically in the presence of pyrite (FeS₂) grains. Then, as much as 10% of the initial methanogenic population survived oxic desiccation. This relatively good resistance is in agreement with observations that methanogens in rice fields survive the periods when the paddy soil is dry and oxic.     

Snow depth, soil freezing, and fluxes of carbon dioxide, nitrous oxide and methane in a northern hardwood forest

Soil–atmosphere fluxes of trace gases (especially nitrous oxide (N₂O)) can be significant during winter and at snowmelt. We investigated the effects of decreases in snow cover on soil freezing and trace gas fluxes at the Hubbard Brook Experimental Forest, a northern hardwood forest in New Hampshire, USA. We manipulated snow depth by shoveling to induce soil freezing, and measured fluxes of N₂O, methane (CH₄) and carbon dioxide (CO₂) in field chambers monthly (bi-weekly at snowmelt) in stands dominated by sugar maple or yellow birch. The snow manipulation and measurements were carried out in two winters (1997/1998 and 1998/1999) and measurements continued through 2000. Fluxes of CO₂ and CH₄ showed a strong seasonal pattern, with low rates in winter, but N₂O fluxes did not show strong seasonal variation. The snow manipulation induced soil freezing, increased N₂O flux and decreased CH₄ uptake in both treatment years, especially during winter. Annual N₂O fluxes in sugar maple treatment plots were 207 and 99 mg N m⁻² yr⁻¹ in 1998 and 1999 vs. 105 and 42 in reference plots. Tree species had no effect on N₂O or CO₂ fluxes, but CH₄ uptake was higher in plots dominated by yellow birch than in plots dominated by sugar maple. Our results suggest that winter fluxes of N₂O are important and that winter climate change that decreases snow cover will increase soil:atmosphere N₂O fluxes from northern hardwood forests.     

Measurement of denitrification in estuarine sediment using membrane inlet mass spectrometry

Abstract Denitrification was measured in intact sediment cores and in homogenised slurries using membrane inlet mass spectrometry. Dissolved concentrations of O₂, N₂, N₂O and CO₂ were simultaneously monitored. Using a 0.8 mm diameter needle probe, a comparison was made of the gas profiles of intact cores obtained under different conditions, i.e. with air or argon as the headspace gas and after the addition of nitrate and/or a carbon source to the sediment surface. O₂ was detectable to a depth of 1 cm under a headspace of air and the depth at which the maxima of denitrification products occurred was 1.5–2 cm. Denitrification products (N₂O, N₂) occurred in the surface layers where O₂ was above the minimum level of detectability (> 0.25 μM): diffusion of N₂ and N₂O upwards from the anoxic zone, local anaerobic microenvironments or aerobic denitrification are alternative explanations for this observation. The addition of nitrate and/or acetate increased the concentrations of N₂, N₂O and CO₂ in the sediment core. In sediment slurries, the pH, nitrate concentration, carbon source and the depth from which the sample was taken affected the rate of denitrification. Nitrogen was the sole detectable end product. Maximum denitrification occurred at pH 7.5 and at 20 mM nitrate. Denitrification was at a maximum in those slurries prepared from sections of core at 1–2 cm depth.     

Direct mass spectrometric measurement of gases in peat cores

Abstract Dissolved gas concentrations (O₂, CH₄, CO₂) in peat cores were monitored simultaneously using a fine (1.56 mm diameter) membrane inlet probe connected to a quadrupole mass spectrometer. This technique allows direct measurements at specific locations within the sample with minimal disturbance. Detailed gas profiles in completely waterlogged peat samples (hollows) and samples in which the water table was several cm below the vegetation surface (hummocks) were compared. The depth of the water table played a central role in the distribution of gases. In a hollow, oxygen was present (90 μM) at the surface but was not detectable (<0.5 μM) at depths greater than 2 cm. Concentrations of CH₄ and CO₂ increased from 6 and 300 μM respectively at the surface to maxima of 450 and 3900 μM at 13 cm depth. At a hummock, O₂ and CO₂ were present above the water table but CH₄ was not detectable. CH₄ was measurable 2 cm below the water table. Both CH₄ and CO₂ concentrations increased with depth but maxima were not attained in the sampled cores.     

A review of nitrogen enrichment effects on three biogenic GHGs: the CO2 sink may be largely offset by stimulated N2O and CH4 emission

Anthropogenic nitrogen (N) enrichment of ecosystems, mainly from fuel combustion and fertilizer application, alters biogeochemical cycling of ecosystems in a way that leads to altered flux of biogenic greenhouse gases (GHGs). Our meta-analysis of 313 observations across 109 studies evaluated the effect of N addition on the flux of three major GHGs: CO₂, CH₄ and N₂O. The objective was to quantitatively synthesize data from agricultural and non-agricultural terrestrial ecosystems across the globe and examine whether factors, such as ecosystem type, N addition level and chemical form of N addition influence the direction and magnitude of GHG fluxes. Results indicate that N addition increased ecosystem carbon content of forests by 6%, marginally increased soil organic carbon of agricultural systems by 2%, but had no significant effect on net ecosystem CO₂ exchange for non-forest natural ecosystems. Across all ecosystems, N addition increased CH₄ emission by 97%, reduced CH₄ uptake by 38% and increased N₂O emission by 216%. The net effect of N on the global GHG budget is calculated and this topic is reviewed. Most often N addition is considered to increase forest C sequestration without consideration of N stimulation of GHG production in other ecosystems. However, our study indicated that although N addition increased the global terrestrial C sink, the CO₂ reduction could be largely offset (53–76%) by N stimulation of global CH₄ and N₂O emission from multiple ecosystems.     

Consumption of NO by methanotrophic bacteria in pure culture and in soil

Abstract The methanotrophs Methylomonas angile (type I) and Methylosinus trichosporium (type II) produced nitrite, nitrate and N₂O during growth on methane, apparently by heterotrophic nitrification of ammonium. The methanotrophs were also able to consume NO but did not produce it. After incubation of soil from a drained paddy field in the presence of CH₄ the numbers of methanotrophs increased from 10⁵ to 10⁷ per gram dry weigth. The thus enriched soil showed increased rates of NO consumption while rates of NO production did not change.     

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

Abstract Turnover times of radioactive glucose were shorter in paddy soil (4–16 min) than in Lake Constance sediment (18–62 min). In the paddy soil, 65–75% of the radioactive glucose was converted to soluble metabolites. In the sediment, only about 25% of the radioactive glucose was converted to soluble metabolites, the rest to particulate material. In anoxic paddy soil, the degradation pattern of position-labelled glucose was largely consistent with glucose degradation via the Embden-Meyerhof-Parnas (EMP) pathway followed by methanogenic acetate cleavage: CO₂ mainly originated from C-3,4, whereas CH₄ mainly originated from C-1 and C-6 of glucose. Acetate-carbon originated from C-1, C-2 and C-6 rather than from C-3,4 of glucose. In both paddy soil and Lake Constance sediment acetate and CO₂ were the most important early metabolites of radioactive glucose. Other early products included propionate, ethanol/butyrate, succinate, and lactate, but accounted each for less than 1–8% of the glucose utilized. The labelling of propionate by [3,4-¹⁴C]glucose suggests that it was mainly produced from glucose or lactate rather than from ethanol. Isopropanol and caproate were also detectable in paddy soil, but were not produced from radioactive glucose. Chloroform inhibited methanogenesis, inhibited the further degradation of radioactive acetate and resulted in the accumulation of H₂, however, did not inhibit glucose degradation. Since acetate was the main soluble fermentation product of glucose and was produced at a relatively high molar acetate: CO₂ ratio (2.5:1), homoacetogenesis appeared to be the most important glucose fermentation pathway.     

Reduction of nitrous oxide by a soil Cytophaga in the presence of acetylene and sulfide

Abstract A denitrifying Cytophaga was isolated from soil enriched by anaerobic incubation with glucose, sulfide (S²⁻), nitrous oxide (N₂O), and acetylene (C₂H₂). Such soil enrichments and pure cultures of the isolated Cytophaga reduced N₂O rapidly even in the presence of a normally inhibitory concentration of C₂H₂ (4 kPa) providing S²⁻ was present (8 μmol/g soil or 0.4 μmol/ml culture). Since C₂H₂ inhibition of the reduction of N₂O is used as a tool in the assay of denitrification, the presence in large numbers of such a Cytophaga may influence the effectiveness of this assay especially in sulfidic environments.     

Methane-dependent nitrate production by a microbial consortium enriched from a cultivated humisol

Abstract A consortium was enriched from a humisol incubated with 3.6 kPa CH₄ and NH₄⁺. This consortium oxidized NH₄⁺ to NO₂⁻ and NO₃⁻ (NO₃⁻/NO₂⁻ ratio about 20) with smaller amounts of N₂O. This oxidation stopped in the stationary phase after depletion of CH₄. CH₃OH or CO₂ did not support oxidation. Growth and resting cell experiments suggested that nitrification was associated with methanotrophic activity and that chemoautotrophic nitrifiers were absent.     

Hydrogen Production by Rumen Holotrich Protozoa: Effects of Oxygen and Implications for Metabolic Control by In Situ Conditions

Experiments with washed suspensions of holotrich protozoa (Isotricha spp. and Dasytricha ruminantium ) showed that both organisms have an efficient 0,-scavenging capability (apparent K_m values 2.3 and 0.3 μM, respectively). Reversible inhibition of H₂, production increased almost linearly with increasing O₂ up to 1.5 μM; higher levels of O₂ gave irreversible inhibition. In situ determinations of H, CH₄, O₂, and CO₂, in ovine rumen liquor, using a membrane inlet mass spectrometer probe, indicated that O₂, was present before feeding at 1-1.5 μM and decreased to undetectable levels (<0.25 μM) within 25 min after feeding. A transient increase in O₂. concentration after feeding occurred only in defaunated animals and resulted in suppression of CH₄ and CO₂ production. The presence of washed holotrich protozoa decreases the O₂ sensitivity of CH₄ production by suspensions of a cultured methanogenic bacterium Methanosarcina barkeri . It is concluded that holotrich protozoa play a role in ruminal O₂ utilization as well as in the production of fermentation end products (especially short-chain volatile fatty acids) utilized by the ruminant and H, utilized by methanogenic bacteria. These hydrogenosome-containing protozoa thus both control patterns of fermentation by influencing O₂ levels, and are themselves regulated by the low ambient O₂ concentrations they experience in the rumen.     

Bicarbonate-dependent production and methanogenic consumption of acetate in anoxic paddy soil

Abstract Acetate turnover was measured in slurries of anoxic methanogenic paddy soil after addition of carrier-free [2-¹⁴C]-acetate. Acetate concentrations stayed fairly constant for about 1–2 days indicating steady state between production and consumption reactions. Depending on the experiment, acetate concentrations were between 100 and 3000 μM. Turnover rates were determined from the logarithmic decrease of [2-¹⁴C]-acetate or from the accumulation of acetate in the presence of chloroform resulting in similar values, i.e. 12–13 nmol h⁻¹g⁻¹d.w. soil at 17°C and 36–88 nmol h⁻¹g⁻¹d.w. at 30°C. Acetate consumption was completely inhibited by chloroform. The respiratory index (RI) was < 0.27. Hence, acetate was apparently consumed by methanogenic bacteria. About 80–90% of the CH₄ produced originated from the methyl group of acetate. The role of homoacetogenesis for acetate production was studied by measuring the incorporation of radioactive bicarbonate into acetate. In different experiments, CO₂ incorporation accounted for fractions of 1–60% of the acetate produced, about 10% being the most likely value for steady-state conditions. The fraction increased at high H₂ concentrations and decreased at high acetate concentrations. The rate of H₂ production that was required for chemolithotrophic acetate production from CO₂ was two orders of magnitude higher than the actually measured rate. Hence, most of the CO₂ incorporation into acetate was caused by electron donors other than H₂ (e.g., carbohydrates) and/or by exchange reactions.     

Fixation of molecular nitrogen by Methanosarcina barkeri

Abstract Methanosarcina barkeri cells were observed in ammonia-free anaerobic acetate enrichments for sulfate-reducing bacteria. The capacity of Methanosarcina to grow diazotrophically was proved with a pure culture in mineral media with methanol. The cell yields with N₂ or NH₄⁺ ions as nitrogen source were 2.2 g and 6.1 g dry weight, respectively, per mol of methanol. Growth experiments with ¹⁵N₂ revealed that 84% of the cell nitrogen was derived from N₂. Acetylene was highly toxic to Methanosarcina and only reduced at concentrations lower than 100 μmol dissolved per 1 of medium. Assimilation of N₂ and reduction of acetylene were inhibited by NH₄⁺ ions. The experiments show that N₂ fixation occurs not only in eubacteria but also in archaebacteria. The ecological significance of diazotrophic growth of Methanosarcina is discussed.     

Latitudinal differentiated water table control of carbon dioxide, methane and nitrous oxide fluxes from hydromorphic soils: feedbacks to climate change

The possibility of carbon (C) being locked away from the atmosphere for millennia is given in hydromorphic soils. However, the water-table-dependent feedback from soil organic matter (SOM) decomposition to the climate system is less clear. At least three greenhouse gases are produced: carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O). These gases show emission peaks at different water table positions and have different global warming potentials (GWP), for example a factor of 23 for CH₄ and 296 for N₂O as compared with the equivalent mass of CO₂ on a 100-year time horizon. This review of available annual data on all three gases revealed that the radiative forcing effect of SOM decomposition is principally dictated by CO₂ despite its low GWP. Anaerobic SOM decomposition generally has a lower potential feedback to the climatic system than aerobic SOM decomposition. Concrete values are constrained by a lack of data from tropical and subarctic regions. Furthermore, data on N₂O and on plant effects are generally rare. However, there is a clear latitudinal differentiation for the GWP of soils under anaerobic conditions compared with aerobic conditions when looking at CO₂ and CH₄: in the tropical and temperate regions, the anaerobic GWP showed a range of 25–60% of the aerobic value, but values varied between 80% and 110% in the boreal zone. Hence, particularly in the vulnerable boreal zone, the feedback from ecosystems to climate change will highly depend on plant responses to changing water tables at elevated temperatures.     

Membrane inlet mass spectrometric analysis of N-isotope labelling for aquatic denitrification studies

Abstract: Techniques are described for measuring the isotope distribution in dissolved nitrate and N₂ using membrane inlet mass spectrometry, which allows several gases to be measured in a water sample without the need for any separation steps. The isotope distribution in dissolved nitrate was measured using denitrifying Pseudomonas nautica to reduce the nitrate to N₂ which was then measured by mass spectrometry. Pseudomonas nautica NCIMB 1967 was easily grown in nitrate-limited continuous culture minimising intra- or extracellular nitrate or nitrite pools, and the bioassay was tolerant of a range of salinities. The precision of the bioassay when measuring samples with high ¹⁵NO₃⁻ contents (0.5 μmol) was 0.05 atom%; with 0.1 μmol ¹⁵NO₃⁻, the precision was around 0.2 atom%. Differences in labelling of N₂ in preserved samples obtained from ¹⁵NO₃⁻ incubations of water-covered sediment cores were measured on parallel samples with membrane inlet MS and GC-MS. The membrane inlet technique was accurate but the precision on ratio measurements was lower than by GC-MS.     

Effect of algal deposition on acetate and methane concentrations in the profundal sediment of a deep lake (Lake Constance)

Abstract In the profundal sediment ot Lake Constance (143 m depth) the temperature is constant at 4 °C. Despite the constant temperature, CH₄ concentrations changed with season between about 120 μM in winter and about 750 μM in summer, measured down to 30 cm depth. The acetate concentration profiles also varied between seasons. In summer, acetate concentration reached a maximum at about 100 μM in 2 or 4 cm depth. In winter, maximal concentrations of about 5 μM were observed over the entire depth. Input of organic material in late spring may be the reason for the seasonal change of both compounds. To simulate such a sedimentation event, intact sediment cores were covered with suspensions of Porphyridium aerugenium or Synechococcus sp. The addition of the phytoplankton material resulted in a drastic increase of acetate concentrations with a maximum at 2 cm depth, similar to in situ acetate concentrations measured in summer. The same applies for CH₄ for which increased concentrations were observed down to 6 cm depth. H₂ concentrations, on the other hand, showed no distinct increase. Treatment of intact sediment cores with ¹⁴C-labeled Synechococcus cells resulted in the formation of ¹⁴C-acetate, ¹⁴CH₄ and ¹⁴CO₂. Maximum concentrations of ¹⁴CH₄ were found at 4 cm depth, i.e. just above the depth to which ¹⁴C-acetate penetrated. The results show that phytoplankton blooms may cause a seasonal variation of acetate and CH₄ in profundal sediments of deep lakes despite the constant low temperature. They also indicate that acetate is the dominant substrate for methanogenic bacteria in the profundal sediments of Lake Constance.     

FREEZE-BLOWING: A NEW TECHNIQUE FOR THE STUDY OF BRAIN IN VIVO

Abstract— A new apparatus is described which removes and freezes brains of conscious rats more rapidly than was heretofore possible. The apparatus consists of two probes which are driven simultaneously into the cranial vault of the rat immobilized in a specially constructed restraining cage. When in position, air under pressure enters through one probe and blows the supratentorial portion of the brain tissue (situated between the olfactory bulbs and the superior colliculi) out the other probe and into a thin chamber previously cooled in liquid N₂. This method stops brain tissue metabolism more rapidly than the previously-described methods of microwave irradiation, decapitation into liquid N₂, or whole-animal immersion into liquid N₂, as evidenced by the measurement of labile metabolites and redox states. Thus, samples of freeze-blown brain had higher levels of a-oxoglutarate, creatine phosphate, pyruvate, glucose and glucose-6-phosphate and lower levels of lactate, malate and AMP than brain tissue obtained by the other methods. The free cytoplasmic [NAD⁺]/[NADH₂], [NADP⁺]/[NADPH₂] and [ATP]/[ADP] [HPO₄^2-] ratios were higher in freeze-blown samples. These data indicate that more extensive anoxic metabolism occurred when methods other than freeze-blowing were used. We conclude that the levels of metabolites measured in brain obtained with the freeze-blowing technique more closely resemble those which occur in vivo.     

Effect of dilution on methanogenesis, hydrogen turnover and interspecies hydrogen transfer in anoxic paddy soil

Abstract Dilution of anoxic slurries of paddy soil resulted in a proportional decrease of the rates of total methanogenesis and the rate constants of H₂ turnover per gram soil. Dilution did not affect the fraction of H₂/CO₂-dependent methanogenesis which made up 22% of total CH₄ production. However, dilution resulted in a ten fold decrease of the H₂ steady state partial pressure from approximately 4 to 0.4 Pa indicating that H₂/CO₂-dependent methanogenesis was more or less independent of the H₂ pool. The rates of H₂ production calculated from the H₂ turnover rate constants and the H₂ steady state partial pressures accounted for only < 5% of H₂/CO₂-dependent methanogenesis in undiluted soil slurries and for even less after dilution. Upon dilution, the Gibbs free energy available for H₂/CO₂-dependent methanogenesis decreased from −28.4 to only −5.6 kJ per mol. The results indicate that methane was mainly produced from interspecies H₂ transfer within syntrophic bacterial associations and was not significantly affected by the outside H₂ pool.