Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation.

Mechanisms controlling CO2 and CH4 production in wetlands are central to understanding carbon cycling and greenhouse gas exchange. However, the volatility of these respiration products complicates quantifying their rates of production in the field. Attempts to circumvent the challenges through closed system incubations, from which gases cannot escape, have been used to investigate bulk in situ geochemistry. Efforts towards mapping mechanistic linkages between geochemistry and microbiology have raised concern regarding sampling and incubation-induced perturbations. Microorganisms are impacted by oxygen exposure, increased temperatures and accumulation of metabolic products during handling, storage, and incubation. We probed the extent of these perturbations, and their influence on incubation results, using high-resolution geochemical and microbial gene-based community profiling of anaerobically incubated material from three wetland habitats across a permafrost peatland. We compared the original field samples to the material anaerobically incubated over 50 days. Bulk geochemistry and phylum-level microbiota in incubations largely reflected field observations, but divergence between field and incubations occurred in both geochemistry and lineage-level microbial composition when examined at closer resolution. Despite the changes in representative lineages over time, inferred metabolic function with regards to carbon cycling largely reproduced field results suggesting functional consistency. Habitat differences among the source materials remained the largest driver of variation in geochemical and microbial differences among the samples in both incubations and field results. While incubations may have limited usefulness for identifying specific mechanisms, they remain a viable tool for probing bulk-scale questions related to anaerobic C cycling, including CO2 and CH4 dynamics.

Characterization of Bacterial and Fungal Communities Reveals Novel Consortia in Tropical Oligotrophic Peatlands.

Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions within peatlands can regulate greenhouse gas production, organic matter turnover, and nutrient cycling. Here we analyze bacterial and fungal communities along a steep P gradient in a tropical peat dome and investigate community level traits and network analyses to better understand the composition and potential interactions of microorganisms in these understudied systems and their relationship to peatland biogeochemistry. We found that both bacterial and fungal community compositions were significantly different along the P gradient, and that the low-P bog plain was characterized by distinct fungal and bacterial families. At low P, the dominant fungal families were cosmopolitan parasites and endophytes, including Clavicipitaceae (19%) in shallow soils (0-4 cm), Hypocreaceae (50%) in intermediate-depth soils (4-8 cm), and Chaetothyriaceae (45%) in deep soils (24-30 cm). In contrast, high- and intermediate-P sites were dominated by saprotrophic families at all depths. Bacterial communities were consistently dominated by the acidophilic Koribacteraceae family, with the exception of the low-P bog site, which was dominated by Acetobacteraceae (19%) and Syntrophaceae (11%). These two families, as well as Rhodospirillaceae, Syntrophobacteraceae, Syntrophorhabdaceae, Spirochaetaceae, and Methylococcaceae appeared within low-P bacterial networks, suggesting the presence of a syntrophic-methanogenic consortium in these soils. Further investigation into the active microbial communities at these sites, when paired with CH4 and CO2 gas exchange, and the quantification of metabolic intermediates will validate these potential interactions and provide insight into microbially driven biogeochemical cycling within these globally important tropical peatlands.

Massive peatland carbon banks vulnerable to rising temperatures.

Peatlands contain one-third of the world's soil carbon (C). If destabilized, decomposition of this vast C bank could accelerate climate warming; however, the likelihood of this outcome remains unknown. Here, we examine peatland C stability through five years of whole-ecosystem warming and two years of elevated atmospheric carbon dioxide concentrations (eCO2). Warming exponentially increased methane (CH4) emissions and enhanced CH4 production rates throughout the entire soil profile; although surface CH4 production rates remain much greater than those at depth. Additionally, older deeper C sources played a larger role in decomposition following prolonged warming. Most troubling, decreases in CO2:CH4 ratios in gas production, porewater concentrations, and emissions, indicate that the peatland is becoming more methanogenic with warming. We observed limited evidence of eCO2 effects. Our results suggest that ecosystem responses are largely driven by surface peat, but that the vast C bank at depth in peatlands is responsive to prolonged warming.

Stability of peatland carbon to rising temperatures.

Peatlands contain one-third of soil carbon (C), mostly buried in deep, saturated anoxic zones (catotelm). The response of catotelm C to climate forcing is uncertain, because prior experiments have focused on surface warming. We show that deep peat heating of a 2 m-thick peat column results in an exponential increase in CH4 emissions. However, this response is due solely to surface processes and not degradation of catotelm peat. Incubations show that only the top 20-30 cm of peat from experimental plots have higher CH4 production rates at elevated temperatures. Radiocarbon analyses demonstrate that CH4 and CO2 are produced primarily from decomposition of surface-derived modern photosynthate, not catotelm C. There are no differences in microbial abundances, dissolved organic matter concentrations or degradative enzyme activities among treatments. These results suggest that although surface peat will respond to increasing temperature, the large reservoir of catotelm C is stable under current anoxic conditions.

Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the Glacial Lake Agassiz Peatland.

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites.

Improved field methods to quantify methane oxidation in landfill cover materials using stable carbon isotopes.

Stable carbon isotopes provide a robust approach toward quantification of methanotrophic activity in landfill covers. The field method often applied to date has compared the delta13C of emitted to anaerobic zone CH4. Recent laboratory mass balance studies have indicated thatthis approach tends to underestimate CH4 oxidation. Therefore, we examined the CH4-delta13C at various soil depths in field settings and compared these values to emitted CH4. At 5-10 cm depth, we observed the most enrichment in CH4-delta13C (-46.0 to -32.1 per thousand). Emitted CH4-delta13C was more negative, ranging from -56.5 to -43.0 per thousand. The decrease in CH4-delta13C values from the shallow subsurface to the surface is the result of processes that result in selective emission of 12CH4 and selective retention of 13CH4 within the soil. Seasonal percent oxidation was calculated at seven sites representing four cover materials. Probe samples averaged greater (21 +/- 2%, p < 0.001, n = 7) oxidation than emitted CH4 data. We argue that calculations of fraction oxidized based on soil derived CH4 should yield upper limit values. When considered with emitted CH4 values, this combined approach will more realistically bracket the actual oxidation value. Following this guideline, we found the percent oxidation to be 23 +/- 3% and 38 +/- 16% for four soil and three compost covers, respectively.

Atmospheric emissions and attenuation of non-methane organic compounds in cover soils at a French landfill.

In addition to methane (CH(4)) and carbon dioxide (CO(2)), landfill gas may contain more than 200 non-methane organic compounds (NMOCs) including C(2+)-alkanes, aromatics, and halogenated hydrocarbons. Although the trace components make up less than 1% v/v of typical landfill gas, they may exert a disproportionate environmental burden. The objective of this work was to study the dynamics of CH(4) and NMOCs in the landfill cover soils overlying two types of gas collection systems: a conventional gas collection system with vertical wells and an innovative horizontal gas collection layer consisting of permeable gravel with a geomembrane above it. The 47 NMOCs quantified in the landfill gas samples included primarily alkanes (C(2)-C(10)), alkenes (C(2)-C(4)), halogenated hydrocarbons (including (hydro)chlorofluorocarbons ((H)CFCs)), and aromatic hydrocarbons (BTEXs). In general, both CH(4) and NMOC fluxes were all very small with positive and negative fluxes. The highest percentages of positive fluxes in this study (considering all quantified species) were observed at the hotspots, located mainly along cell perimeters of the conventional cell. The capacity of the cover soil for NMOC oxidation was investigated in microcosms incubated with CH(4) and oxygen (O(2)). The cover soil showed a relatively high capacity for CH(4) oxidation and simultaneous co-oxidation of the halogenated aliphatic compounds, especially at the conventional cell. Fully substituted carbons (TeCM, PCE, CFC-11, CFC-12, CFC-113, HFC-134a, and HCFC-141b) were not degraded in the presence of CH(4) and O(2). Benzene and toluene were also degraded with relative high rates. This study demonstrates that landfill soil covers show a significant potential for CH(4) oxidation and co-oxidation of NMOCs.

Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology.

Antarctic permafrost soils have not received as much geocryological and biological study as has been devoted to the ice sheet, though the permafrost is more stable and older and inhabited by more microbes. This makes these soils potentially more informative and a more significant microbial repository than ice sheets. Due to the stability of the subsurface physicochemical regime, Antarctic permafrost is not an extreme environment but a balanced natural one. Up to 10(4) viable cells/g, whose age presumably corresponds to the longevity of the permanently frozen state of the sediments, have been isolated from Antarctic permafrost. Along with the microbes, metabolic by-products are preserved. This presumed natural cryopreservation makes it possible to observe what may be the oldest microbial communities on Earth. Here, we describe the Antarctic permafrost habitat and biodiversity and provide a model for martian ecosystems.

Methane oxidation in biofilters measured by mass-balance and stable isotope methods.

Simultaneous flux and isotope measurements on compost and sand biofilters showed that the fraction of CH4 oxidized, calculated from delta13C measurements using a closed system model (f(oxir,C)), averaged only 0.455 of the fraction oxidized based on mass-balance measurements (f(oxm)). The discrepancy between f(oxm) and f(oxir,C) may be partly due to complete oxidation of a portion of the inflow gas, thereby eliminating its contribution to the emitted methane on which isotopic measurements are conducted. To relate f(oxir,C) and f(oxm) a simple binary closed-system model is proposed that assumes that f(oxir,C) refers to only part of the inflow, P, and that the remainder of inflow (1 - P) is completely oxidized before reaching the outlet. This model is compared to the standard open-system model. The H-isotope fraction oxidized (f(oxir,H)) was determined for a subset of samples and found to be not significantly different from f(oxir,C). The carbon isotope fractionation factor, alphaox,C = 1.0244, and the H-isotope fractionation factor, alphaox,H = 1.2370, were determined by incubation studies. Delta13C measurements indicated that the emitted flow was more strongly oxidized by the compost biofilters (f(oxir,C) = 0.362, f(oxm) = 0.757) than the sand biofilters (f(oxir,C) = 0.222, f(oxm) = 0.609).

Methane bubbling from Siberian thaw lakes as a positive feedback to climate warming.

Large uncertainties in the budget of atmospheric methane, an important greenhouse gas, limit the accuracy of climate change projections. Thaw lakes in North Siberia are known to emit methane, but the magnitude of these emissions remains uncertain because most methane is released through ebullition (bubbling), which is spatially and temporally variable. Here we report a new method of measuring ebullition and use it to quantify methane emissions from two thaw lakes in North Siberia. We show that ebullition accounts for 95 per cent of methane emissions from these lakes, and that methane flux from thaw lakes in our study region may be five times higher than previously estimated. Extrapolation of these fluxes indicates that thaw lakes in North Siberia emit 3.8 teragrams of methane per year, which increases present estimates of methane emissions from northern wetlands (< 6-40 teragrams per year; refs 1, 2, 4-6) by between 10 and 63 per cent. We find that thawing permafrost along lake margins accounts for most of the methane released from the lakes, and estimate that an expansion of thaw lakes between 1974 and 2000, which was concurrent with regional warming, increased methane emissions in our study region by 58 per cent. Furthermore, the Pleistocene age (35,260-42,900 years) of methane emitted from hotspots along thawing lake margins indicates that this positive feedback to climate warming has led to the release of old carbon stocks previously stored in permafrost.

Methane mass balance at three landfill sites: what is the efficiency of capture by gas collection systems?

Many developed countries have targeted landfill methane recovery among greenhouse gas mitigation strategies, since methane is the second most important greenhouse gas after carbon dioxide. Major questions remain with respect to actual methane production rates in field settings and the relative mass of methane that is recovered, emitted, oxidized by methanotrophic bacteria, laterally migrated, or temporarily stored within the landfill volume. This paper presents the results of extensive field campaigns at three landfill sites to elucidate the total methane balance and provide field measurements to quantify these pathways. We assessed the overall methane mass balance in field cells with a variety of designs, cover materials, and gas management strategies. Sites included different cell configurations, including temporary clay cover, final clay cover, geosynthetic clay liners, and geomembrane composite covers, and cells with and without gas collection systems. Methane emission rates ranged from -2.2 to >10,000 mg CH(4) m(-2) d(-1). Total methane oxidation rates ranged from 4% to 50% of the methane flux through the cover at sites with positive emissions. Oxidation of atmospheric methane was occurring in vegetated soils above a geomembrane. The results of these studies were used as the basis for guidelines by the French environment agency (ADEME) for default values for percent recovery: 35% for an operating cell with an active landfill gas (LFG) recovery system, 65% for a temporary covered cell with an active LFG recovery system, 85% for a cell with clay final cover and active LFG recovery, and 90% for a cell with a geomembrane final cover and active LFG recovery.

Partitioning microbial respiration between jet fuel and native organic matter in an organic-rich long time-contaminated aquifer.

The relative importance of jet fuel biodegradation relative to the respiration of natural organic matter in a contaminated organic-rich aquifer underlying a fire training area at Tyndall Air Force Base, Florida, USA was determined with isotopic measurements. Thirteen wells were sampled and analyzed for BTX (benzene, toluene, xylene), dissolved inorganic carbon (DIC) and CH4 concentrations, and delta13C and 14C of DIC. Results range from non-detectable to 3790 ppb, 1.4-24 mM, 0.2-776 microM, +5.8 per thousand to -22 per thousand, and from 52 to 99 pmc, respectively. Residual fuel was confined to two center wells underlying the fire training area. DIC and CH4 concentrations were elevated down-gradient of the contamination, but also at sites that were not in the apparent flow path of the contaminated groundwater. DIC exhibited greatest delta13C enrichment at highest DIC and CH4 concentrations indicating that CH4 production was an important respiration mode. Radiocarbon-depleted DIC was observed at sites with high hydrocarbon concentrations and down-gradient of the site. The results indicate that while natural attenuation was not rapidly reducing the quantity of free product overlying the aquifer at the site of contamination, it was at least constraining its flow away from the spill site. Apparently under the conditions of this study, BTX was degraded as rapidly as it was dissolved.

Evaluation of a biologically active cover for mitigation of landfill gas emissions.

Landfills are the third largest source of anthropogenic CH4 in the United States, and there is potential for reduction in this source of greenhouse gases and other contaminants. The objective of this work was to contrast emissions of CH4 and non-methane organic compounds (NMOCs) from landfill cells covered with soil or a biologically active cover consisting of yard waste compost. On the basis of four field campaigns over 14 months, CH4 emissions from the biocover (BC) varied from -1.73 to 1.33 g m(-2) d(-1), with atmospheric uptake measured in 52% of tests. BC emissions did not increase when the gas collection system was turned off. Uptake of atmospheric CH4 was measured in 54% of tests on the soil cover (SC) when the gas collection was system active and 12% when the gas collection system was off. Many (26%) relatively high fluxes (>15 g m(-2) d(-1)) were measured from the SC as were some dramatic effects due to deactivation of the gas collection system. In tests with positive emissions, stable isotope measurements showed that the BC and SC were responsible for oxidation of 55% and 21% of the CH4 reaching the bottom of the respective cover. Seven of the highest 10 NMOC emissions were measured in the SC, and 17 of 21 fluxes for speciated organic compounds were higher in the SC. The relationship between CH4, NMOC, and individual organic compound emissions suggested a correlation between CH4 and trace organic oxidation. BCs can reduce landfill gas emissions in the absence of a gas collection system and can serve as a polishing step in the presence of an active system.

Enhancement of orimulsion biodegradation through the addition of natural marine carbon substrates.

Orimulsion is a bitumen-based heavy fuel that is a less expensive alternative to traditional fuel oils. However, because its density is intermediate between that of freshwater and seawater, in the event of a spill, the fuel could strand in the sediments. Previous work indicated that only 0.6-2.7% of the bitumen would degrade in long incubations of marine sediments. We added various natural carbon substrates to stimulate the degradation of bitumen by native populations of benthic bacteria. The concentration and carbon isotopic signature of the respired carbon dioxide was measured to partition the substrates that supported bacterial respiration. We found that the addition of seagrass and pinfish stimulated the degradation of bitumen by as much as 2-9-fold relative to incubations without these substrates. Biodegradation of bitumen may be enhanced by the addition of natural marine carbon substrates and may be a useful approach for bioremediation. Preadaptation of the bacteria to bitumen did not significantly enhance their ability to degrade it.

Field measurements of internal pressurization in Phragmites australis (Poaceae) and implications for regulation of methane emissions in a midlatitude prairie wetland.

Emergent aquatic macrophytes in vegetated wetlands provide routes for methane (CH(4)) transport from sites of production in oxygen-poor sediments, where CH(4) concentrations are relatively high, to the atmosphere, which typically has much lower CH(4) concentrations. Transport can occur through aerenchymatous tissue via simple diffusion. Recently, the importance of convective throughflow (i.e., mass transport of gases through plants driven by pressure gradients) in enhancing gas transport has been demonstrated in several genera (e.g., Nuphar, Nymphaea, Nelumbo, Typha, and Phragmites). This study was conducted to elucidate the governing plant-mediated gas transport mechanisms in a midlatitude prairie wetland and to determine both their diel and seasonal variations and the importance of environmental controlling factors. Pressures inside culms of the two dominant emergent aquatic macrophytes (Scirpus acutus and Phragmites australis) were measured directly throughout the growing season and on selected days in midseason. Supporting measurements included solar radiation, air temperature, relative humidity, and windspeed. Results indicated pressures inside green healthy culms of Phragmites were above atmospheric pressure by up to 1650 Pa during the day. At night culm pressures were at or slightly above atmospheric. No pressurization was detected in Scirpus. Highest pressures in Phragmites occurred during midseason when biomass and foliage area index were at their maxima (920 g/m(2) and 2.8, respectively). High internal pressures also coincided with periods of high solar radiation (>500 W/m(2)), high temperature (>20°C), and low relative humidity (<60%). Periods of high internal pressures also coincided with periods of high CH(4) efflux from the wetland as measured in concomitant studies. Convective throughflow driven by internal pressure gradients in Phragmites thus explains much of the diel variation in methane efflux previously reported from this wetland.