Links between methanotroph community composition and CH4 oxidation in a pine forest soil

The main gap in our knowledge about what determines the rate of CH₄ oxidation in forest soils is the biology of the microorganisms involved, the identity of which remains unclear. In this study, we used stable-isotope probing (SIP) following ¹³CH₄ incorporation into phospholipid fatty acids (PLFAs) and DNA/RNA, and sequencing of methane mono-oxygenase ( pmoA ) genes, to identify the influence of variation in community composition on CH₄ oxidation rates. The rates of ¹³C incorporation into PLFAs differed between horizons, with low ¹³C incorporation in the organic soil and relatively high ¹³C incorporation into the two mineral horizons. The microbial community composition of the methanotrophs incorporating the ¹³C label also differed between horizons, and statistical analyses suggested that the methanotroph community composition was a major cause of variation in CH₄ oxidation rates. Both PLFA and pmoA -based data indicated that CH₄ oxidizers in this soil belong to the uncultivated 'upland soil cluster α'. CH₄ oxidation potential exhibited the opposite pattern to ¹³C incorporation, suggesting that CH₄ oxidation potential assays may correlate poorly with in situ oxidation rates. The DNA/RNA-SIP assay was not successful, most likely due to insufficient ¹³C-incorporation into DNA/RNA. The limitations of the technique are briefly discussed.     

Effects of raised CO2 on potential CH4 production and oxidation in, and CH4 emission from, a boreal mire

1 In a glasshouse experiment we studied the effect of raised CO₂ concentration (720 p.p.m.) on CH₄ emission at natural boreal peat temperatures using intact cores of boreal peat with living vascular plants and Sphagnum mosses. After the end of the growing season half of the cores were kept unnaturally warm (17–20 °C). The potential for CH₄ production and oxidation was measured at the end of the emission experiment.
2 The vascular cores ('Sedge') consisted of a moss layer with sedges, and the moss cores (' Sphagnum ') of Sphagnum mosses (some sedge seedlings were removed by cutting). Methane efflux was 6–12 times higher from the Sedge cores than from the Sphagnum cores. The release of CH ₄ from Sedge cores increased with increasing temperature of the peat and decreased with decreasing temperature. Methane efflux from Sphagnum cores was quite stable independent of the peat temperatures.
3 In both Sedge and Sphagnum samples, CO₂ treatment doubled the potential CH₄ production but had no effect on the potential CH₄ oxidation. A raised concentration of CO₂ increased CH₄ efflux weakly and only at the highest peat temperatures (17–20 °C).
4 The results suggest that in cool regions, such as boreal wetlands, temperature would restrict decomposition of the extra substrates probably derived from enhanced primary production of mire vegetation under raised CO₂ concentrations, and would thus retard any consequent increase in CH₄ emission.     

Seasonal variation in pathways of CH4 production and in CH4 oxidation in rice fields determined by stable carbon isotopes and specific inhibitors

Flooded rice fields, which are an important source of the atmospheric methane, have become a model system for the study of interactions between various microbial processes. We used a combination of stable carbon isotope measurements and application of specific inhibitors in order to investigate the importance of various methanogenic pathways and of CH₄ oxidation for controlling CH₄ emission. The fraction of CH₄ produced from acetate and H₂/CO₂ was calculated from the isotopic signatures of acetate, carbon dioxide (CO₂) and methane (CH₄) measured in porewater, gas bubbles, in the aerenchyma of the plants and/or in incubation experiments. The calculated ratio between both pathways reflected well the ratio determined by application of methyl fluoride (CH₃F) as specific inhibitor of acetate‐dependent methanogenesis. Only at the end of the season, the theoretical ratio of acetate: H₂ = 2 : 1 was reached, whereas at the beginning H₂/CO₂‐dependent methanogenesis dominated. The isotope discrimination was different between rooted surface soil and unrooted deep soil. Root‐associated CH₄ production was mainly driven by H₂/CO₂. Porewater CH₄ was found to be a poor proxy for produced CH₄. The fraction of CH₄ oxidised was calculated from the isotopic signature of CH₄ produced in vitro compared to CH₄ emitted in situ, corrected for the fractionation during the passage from the aerenchyma to the atmosphere. Isotope mass balances and in situ inhibition experiments with difluoromethane (CH₂F₂) as specific inhibitor of methanotrophic bacteria agreed that CH₄ oxidation was quantitatively important at the beginning of the season, but decreased later. The seasonal pattern was consistent with the change of potential CH₄ oxidation rates measured in vitro. At the end of the season, isotope techniques detected an increase of oxidation activity that was too small to be measured with the flux‐based inhibitor technique. If porewater CH₄ was used as a proxy of produced CH₄, neither magnitude nor seasonal pattern of in situ CH₄ oxidation could be reproduced. An oxidation signal was also found in the isotopic signature of CH₄ from gas bubbles that were released by natural ebullition. In contrast, bubbles stirred up from the bulk soil had preserved the isotopic signature of the originally produced CH₄.     

Carbon isotope ratios of plants and occurrences of C4 species under different soil moisture regimes in arid region of Northwest China

Carbon isotope ratio of leaf dry matter, δ ¹³C, was measured on species occurring within Baiyin desert community, consisting of valley, slope and ridge microhabitats, and within Shandan desert community, consisting of Gobi desert and seasonal flooded creek microhabitats, in Northwest China. δ ¹³C of C₃ species increased with a decrease in soil water availability, suggesting that water-use efficiency (WUE) increased with decreasing soil moisture, whereas for all C₄ species, δ ¹³C tended to decrease with decreasing soil water availability, suggesting that WUE also increased with decreasing soil moisture. Above results indicated that water-use pattern was conservative under drought for C₄ and C₃ plants. In this present study, C₄ species' occurrences within different microhabitats were investigated and C₄ plants were observed to be absent and/or scarce within relatively lower soil moisture microhabitats, whereas they occurred and/or even had a high abundance within relatively higher soil moisture microhabitats, suggesting limited moisture available was a key factor of limiting C₄ distribution in arid region of Northwest China.     

Response of methanotrophic activity and community structure to temperature changes in a diffusive CH4/O2 counter gradient in an unsaturated porous medium

Microbial methane oxidation is a key process in the global methane cycle. In the context of global warming, it is important to understand the responses of the methane-oxidizing microbial community to temperature changes in terms of community structure and activity. We studied microbial methane oxidation in a laboratory-column system in which a diffusive CH₄/O₂ counter gradient was maintained in an unsaturated porous medium at temperatures between 4 and 20 °C. Methane oxidation was highly efficient at all temperatures, as on average 99 ± 0.5% of methane supplied to the system was oxidized. The methanotrophic community that established in the model system after initial inoculation appeared to be able to adapt quickly to different temperatures, as methane emissions remained low even after the system was subjected to abrupt temperature changes. FISH showed that Type I as well as Type II methanotrophs were probably responsible for the observed activity in the column system, with a dominance of Type I methanotrophs. Cloning and sequencing suggested that Type I methanotrophs were represented by the genus Methylobacter while Type II were represented by Methylocystis . The results suggest that in an unsaturated system with diffusive substrate supply, direct effects of temperature on apparent methanotrophic activity and community may be of minor importance. However, this remains to be verified in the field.     

Responses of a C3 and a C4 perennial grass to elevated CO2 and temperature under different water regimes

An experiment was carried out to determine the effects of elevated CO₂, elevated temperatures, and altered water regimes in native shortgrass steppe. Intact soil cores dominated by Bouteloua gracilis, a C₄ perennial grass, or Pascopyrum smithii, a C₃ perennial grass, were placed in growth chambers with 350 or 700 μL L^?1 atmospheric CO₂, and under either normal or elevated temperatures. The normal regime mimicked field patterns of diurnal and seasonal temperatures, and the high-temperature regime was 4 °C warmer. Water was supplied at three different levels in a seasonal pattern similar to that observed in the field. Total biomass after two growing seasons was 19% greater under elevated CO₂, with no significant difference between the C₃ and C₄ grass. The effect of elevated CO₂ on biomass was greatest at the intermediate water level. The positive effect of elevated CO₂ on shoot biomass was greater at normal temperatures in B. gracilis, and greater at elevated temperatures in P. smithii. Neither root-to-shoot ratio nor production of seed heads was affected by elevated CO₂. Plant tissue N and soil inorganic N concentrations were lower under elevated Co₂, but no more so in the C₃ than the C₄ plant. Elevated CO₂ appeared to increase plant N limitation, but there was no strong evidence for an increase in N limitation or a decrease in the size of the CO₂ effect from the first to the second growing season. Autumn samples of large roots plus crowns, the perennial organs, had 11% greater total N under elevated CO₂, in spite of greater N limitation.     

Mass spectrometric monitoring of gases (CO2, CH4, O2) in a mesotrophic peat core from Kopparås Mire, Sweden

Membrane inlet mass spectrometry was used to monitor dissolved gas concentrations (CO₂, CH₄ and O₂) in a mesotrophic peat core from Kopparås, Sweden. 1 A comparison of depth profiles (down to 22 cm) with an ombrotrophic peat core (Ellergower, SW Scotland) investigated previously, revealed major differences in gas concentrations. Thus methane reached concentrations more than twice as high (800 μM) at depths greater than 12 cm in the Kopparås core. As shown previously, the primary determinant of the depth of the oxic zone is the level of the water table. Whereas in the Scottish cores, mass spectrometric detectability of O₂ was confined to the first 3 cm below this level, in the Swedish core penetration of O₂ was greater (7 cm). CO₂ profiles were similar in cores from both locations. 2 A thick layer of Sphagnum mosses dominated the plant cover of the Swedish peat core. A poorly developed deep root system, as distinct from that of the vascular plant cover in Scottish cores, diminished gas exchange rates, and presumably aerobic methane oxidation at depth around roots. These characteristics may contribute to the development of discontinuities in gas profiles at depths greater 15 cm as upward gas transport is established predominantly by diffusion and/or ebullition in the Swedish core. 3 Monitoring gas concentrations at the peat surface and at 2 cm depth after changing water tables showed a delayed response of approximately 4 days as a result of the high water content and moisture‐regulating capacity of mosses. 4 Recovery processes at 2 cm depth after raising the water table revealed final production rates of dissolved CO₂ and CH₄ in the peat pore water between 0.8 and 4.4 μmol h^?1 L^?1 and between 0.1 and 1.7 μmol h^?1 L^?1, respectively. Higher production rates were found during the day, indicating a diurnal rhythm due to plant photosynthetic activity even at the low values of photosynthetically active radiation (PAR: 110 μmol s^?1 m^?2) used in the experimental set‐up. 5 In the water‐logged mesotrophic Kopparås core changes of dissolved gas concentrations (DGC) at 3 and 14 cm depth were surface temperature‐dependent rather than light dependent. This suggests that changes of air temperature alters the covering vegetation to increase the conductivity for dissolved gases through vascular plants and to facilitate gas transport by diffusion and/or ebullition.     

Ecosystem–atmosphere exchange of CH4 and N2O and ecosystem respiration in wetlands in the Sanjiang Plain, Northeastern China

Natural wetlands are critically important to global change because of their role in modulating atmospheric concentrations of CO₂, CH₄, and N₂O. One 4‐year continuous observation was conducted to examine the exchanges of CH₄ and N₂O between three wetland ecosystems and the atmosphere as well as the ecosystem respiration in the Sanjiang Plain in Northeastern China. From 2002 to 2005, the mean annual budgets of CH₄ and N₂O, and ecosystem respiration were 39.40 ± 6.99 g C m^?2 yr^?1, 0.124 ± 0.05 g N m^?2 yr^?1, and 513.55 ± 8.58 g C m^?2 yr^?1 for permanently inundated wetland; 4.36 ± 1.79 g C m^?2 yr^?1, 0.11 ± 0.12 g N m^?2 yr^?1, and 880.50 ± 71.72 g C m^?2 yr^?1 for seasonally inundated wetland; and 0.21 ± 0.1 g C m^?2 yr^?1, 0.28 ± 0.11 g N m^?2 yr^?1, and 1212.83 ± 191.98 g C m^?2 yr^?1 for shrub swamp. The substantial interannual variation of gas fluxes was due to the significant climatic variability which underscores the importance of long‐term continuous observations. The apparent seasonal pattern of gas emissions associated with a significant relationship of gas fluxes to air temperature implied the potential effect of global warming on greenhouse gas emissions from natural wetlands. The budgets of CH₄ and N₂O fluxes and ecosystem respiration were highly variable among three wetland types, which suggest the uncertainties in previous studies in which all kinds of natural wetlands were treated as one or two functional types. New classification of global natural wetlands in more detailed level is highly expected.     

The effect of termite biomass and anthropogenic disturbance on the CH4 budgets of tropical forests in Cameroon and Borneo

The exchange of CH₄ between tropical forests and the atmosphere was determined by simultaneously measuring the net CH₄ flux at the soil surface and assessing the flux contribution from soil-feeding termite biomass, both within the soil profile and in mounds. In Cameroon the flux of CH₄ ranged from a net emission of 40.7 ng m^–2 s^–1 to a net CH₄ oxidation of –53.0 ng m^–2 s^–1. Soil-inhabiting termite biomass was significantly correlated with CH₄ flux. Termite mounds emitted up to 2000 ng s^–1 mound^–1. Termite-derived CH₄ emission reduced the soil sink strength by up to 28%. Disturbance also had a strong effect on the soil sink strength, with the average rate of CH₄ oxidation, at – 17.5 ng m^–2 s^–1, being significantly smaller (≈ 36%) at the secondary forest site than the –27.2 ng m^–2 s^–1, observed at the primary forest site. CH₄ budgets calculated for each site indicated that both forests were net sinks for CH₄ at – 6.1 kg ha^–1 y^–1 in the near-primary forest and – 3.1 kg ha^–1 y^–1 in the secondary forest. In Borneo, three forest sites representing a disturbance gradient were examined. CH₄ oxidation rates ranged from 0 to – 32.1 ng m^–2s^–1 and a significant correlation between the net flux and termite biomass was observed only in an undisturbed primary forest, although the biomass was insufficient to cause net emission of CH₄. Rates of CH₄ oxidation were not significantly different across the disturbance gradient but were, however, larger in the primary forest (averaging – 15.4 ng m^–2 s^–1) than in an old-growth secondary forest (–13.9 ng m^–2s^–1) and a young secondary re-growth (– 10.8 ng m^–2s^–1). CH₄ flux from termite mounds ranged from net oxidation in an abandoned mound to a maximum emission of 468 ng s^–1 mound^–1. CH₄ budgets calculated for each site indicated that CH₄ flux from termite mounds had an insignificant effect on the budget of CH₄ at the regional scale at all three forest sites. Annual oxidation rates were – 4.8, – 4.2 and – 3.4 kg ha^–1 y^–1 in the primary, secondary and young secondary forests, respectively.     

Activity and composition of ammonia oxidizing bacterial communities and emission dynamics of NH3 and N2O in a compost reactor treating organic household waste

Aims:  To monitor emissions of NH₃ and N₂O during composting and link these to ammonia oxidation rates and the community structure of ammonia oxidizing bacteria (AOB).
Methods and Results:  A laboratory-scale compost reactor treating organic household waste was run for 2 months. NH₃ emissions peaked when pH started to increase. Small amounts of N₂O and CH₄ were also produced. In total, 16% and less than 1% of the initial N was lost as NH₃-N and N₂O-N respectively. The potential ammonia oxidation rate, determined by a chlorate inhibition assay, increased fourfold during the first 9 days and then remained high. Initially, both Nitrosospira and Nitrosomonas populations were detected using DGGE analysis of AOB specific 16S rRNA fragments. Only Nitrosomonas europaea was detected under thermophilic conditions, but Nitrosospira populations re-established during the cooling phase.
Conclusions:  Thermophilic conditions favoured high potential ammonia oxidation rates, suggesting that ammonia oxidation contributed to reduced NH₃ emissions. Small but significant amounts of N₂O were emitted during the thermophilic phase. The significance of different AOBs detected in the compost for ammonia oxidation is not clear.
Significance and Impact of Study:  This study shows that ammonia oxidation occurs at high temperature composting and therefore most likely reduces NH₃ emissions.     

Climate controls on C3 vs. C4 productivity in North American grasslands from carbon isotope composition of soil organic matter

We analyzed the δ¹³C of soil organic matter (SOM) and fine roots from 55 native grassland sites widely distributed across the US and Canadian Great Plains to examine the relative production of C₃ vs. C₄ plants (hereafter %C₄) at the continental scale. Our climate vs. %C₄ results agreed well with North American field studies on %C₄, but showed bias with respect to %C₄ from a US vegetation database (statsgo ) and weak agreement with a physiologically based prediction that depends on crossover temperature. Although monthly average temperatures have been used in many studies to predict %C₄, our analysis shows that high temperatures are better predictors of %C₄. In particular, we found that July climate (average of daily high temperature and month's total rainfall) predicted %C₄ better than other months, seasons or annual averages, suggesting that the outcome of competition between C₃ and C₄ plants in North American grasslands was particularly sensitive to climate during this narrow window of time. Root δ¹³C increased about 1‰ between the A and B horizon, suggesting that C₄ roots become relatively more common than C₃ roots with depth. These differences in depth distribution likely contribute to the isotopic enrichment with depth in SOM where both C₃ and C₄ grasses are present.     

Leaf blade structure and C4 acid decarboxylation enzymes in xCynochloris spp. (Poaceae), intergeneric hybrids between species of different C4 type

PRENDERGAST, H. D. V., STONE, N. E. & HATTERSLEY, P. W., 1988. Leaf blade structure and C₄ acid decarboxylation enzymes in x Cynochloris spp. (Poaceae), intergeneric hybrids between species of different C₄ type. x Cynochloris macivorii Clifford and Everist and x C. reynoldensis B. K. Simon (Poaceae) are intergeneric C₄ hybrids between Cynodon dactylon (L.) Pers., and NAD-malic enzyme (NAD-ME) species, and two different PEP carboxykinase (PCK) species of Chloris . Parental species of each hybrid species have the 'classical' leaf blade structure of their respective C₄ acid decarboxylation types. The outline of the photosynthetic carbon reduction (PCR or Kranz) bundle sheath and the position of the PCR cell chloroplasts in x Cynochloris are intermediate between those of the parental species, C. macivorii being more like Cynodon dactylon and x C. reynoldensis more like Chloris spp. The PCR chloroplast shape in x C. macivorii and x C. reynoldensis is like that of Cynodon dactylon and Chloris spp., respectively. Differences between the hybrids in their enzyme activities complement these structural differences: x C. macivorii has more NAD—ME and less PCK activity than x C. reynoldensis , although in both species PCK activity is the greater. Both hybrids, however, have a suberized lamella in PCR cell walls as do Chloris spp. The close taxonomic relationship between Cynodon and Chloris make these genera especially suitable for reciprocal crossing experiments aimed at increasing understanding of the genetic relationships between subtypes of the C₄ photosynthetic pathway.     

稻田土壤氧化态有机碳组分变化及其与甲烷排放的关联性

稻田土壤有机碳是甲烷排放的关键底物之一,不同研究者由于采取的有机碳研究方法不同而得出稻田甲烷排放与土壤有机碳关系的结论不一.为明确影响稻田甲烷排放的土壤有机碳组分,设计了稻田施用不同外源有机碳(稻草还田、鸡粪和猪粪)的田间试验,对稻田甲烷排放和土壤有机碳组分的动态变化及其关联性进行监测和分析.结果表明,猪粪处理的甲烷排放与化肥处理无显著差异,而鸡粪和稻草2个处理的甲烷排放分别比化肥增加1.67倍(P＜0.05),2.69倍(P＜0.05);甲烷排放量与土壤易氧化有机碳含量显示相同顺序:稻草＞鸡粪＞猪粪＞化肥;通径分析表明,土壤易氧化有机碳组分1(被33 mmol/L KMnO4氧化的有机碳)与甲烷排放直接相关,其他有机碳组分仅通过组分1间接作用于水稻生育后期甲烷排放,且排放量较低.由此推断,易氧化有机碳组分1是甲烷排放的主要底物,通过有效措施降低肥源中易氧化态有机碳组分1是减排甲烷的关键技术之一.