Activity and community structure of methane-oxidising bacteria in a wet meadow soil

Utilisation of low methane concentrations by methanotrophs

The growing urgency regarding climate change points to methane as a key greenhouse gas for slowing global warming to allow other mitigation measures to take effect. One approach to both decreasing methane emissions and removing methane from air is aerobic methanotrophic bacteria, those bacteria that grow on methane as sole carbon and energy source and require O2. A subset of these methanotrophs is able to grow on methane levels of 1000 parts per million (ppm) and below, and these present an opportunity for developing both environmental- and bioreactor-based methane treatment systems. However, relatively little is known about the traits of such methanotrophs that allow them to grow on low methane concentrations. This review assesses current information regarding how methanotrophs grow on low methane concentrations in the context of developing treatment strategies that could be applied for both decreasing methane emissions and removing methane from air.

Methanobactin from methanotrophs: genetics, structure, function and potential applications

Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.

Legacy effects override soil properties for CO2 and N2O but not CH4 emissions following digestate application to soil

The application of organic materials to soil can recycle nutrients and increase organic matter in agricultural lands. Digestate can be used as a nutrient source for crop production but it has also been shown to stimulate greenhouse gas (GHG) emissions from amended soils. While edaphic factors, such as soil texture and pH, have been shown to be strong determinants of soil GHG fluxes, the impact of the legacy of previous management practices is less well understood. Here we aim to investigate the impact of such legacy effects and to contrast them against soil properties to identify the key determinants of soil GHG fluxes following digestate application. Soil from an already established field experiment was used to set up a pot experiment, to evaluate N2O, CH4 and CO2 fluxes from cattle-slurry-digestate amended soils. The soil had been treated with farmyard manure, green manure or synthetic N-fertilizer, 18 months before the pot experiment was set up. Following homogenization and a preincubation stage, digestate was added at a concentration of 250 kg total N/ha eq. Soil GHG fluxes were then sampled over a 64 day period. The digestate stimulated emissions of the three GHGs compared to controls. The legacy of previous soil management was found to be a key determinant of CO2 and N2O flux while edaphic variables did not have a significant effect across the range of variables included in this experiment. Conversely, edaphic variables, in particular texture, were the main determinant of CH4 flux from soil following digestate application. Results demonstrate that edaphic factors and current soil management regime alone are not effective predictors of soil GHG flux response following digestate application. Knowledge of the site management in terms of organic amendments is required to make robust predictions of the likely soil GHG flux response following digestate application to soil.

Interactive effect of climate factors, biochar and insecticide chlorpyrifos on methane consumption and microbial abundance in a tropical Vertisol

Climate change may increase the pest infestation leading to intensive use of insecticides. However, the effect of insecticide and climate factors on soil methane (CH₄) consumption is less understood. A laboratory experiment was carried out to evaluate the effect of temperature (15 °C, 35 °C, and 45 °C), moisture holding capacity (MHC) (60%, 100%), biochar (0%, 1%) and chlorpyrifos (0 ppm, 10 ppm) on CH₄ consumption and microbial abundance in a tropical Vertisol of central India. Methane consumption rate k (ng CH₄ consumed g^-1 soil d^-1) varied from 0.065 ± 0.005 to 0.608 ± 0.018. Lowest k was in 15 °C-60% moisture holding capacity (MHC)-no biochar and with 10 ppm chlorpyrifos. Highest k was in 35 °C-100% MHC-1% biochar and without (0 ppm) chlorpyrifos. Cumulative CO₂ production (ng CO₂ produced g^-1 soil d^-1) varied from 446 ± 15 to 1989 ± 116. Both CH₄ consumption and CO₂ production peaked in the treatment of 35 °C-100% MHC-1% biochar. Chlorpyrifos inhibited CH₄ consumption irrespective of treatments. Abundance of 16S rRNA of eubacteria (× 10⁶ g^-1 soil) varied from 2.33 ± 0.58 to 85.67 ± 7.00. Abundance of 16S rRNA genes representing Actinomycetes (× 10⁴ g^-1 soil) varied from 7.67 ± 1.53 and pmoA gene (Methanotrophs) (× 10⁵ g^-1 soil) varied from 1.23 ± 0.59 to 34.33 ± 6.51. Chlorpyrifos inhibited abundance of heterotrophic bacteria and methanotrophs but stimulated actinomycetes. Biochar stimulated the CH₄ consumption, CO₂ production and microbial abundance. Study highlighted that use of chlorpyrifos under climate change factors may inhibit CH₄ consumption but the use of biochar may alleviate the negative effect of the chlorpyrifos.

Unexpected stimulation of soil methane uptake as emergent property of agricultural soils following bio-based residue application

Intensification of agriculture to meet the global food, feed, and bioenergy demand entail increasing re-investment of carbon compounds (residues) into agro-systems to prevent decline of soil quality and fertility. However, agricultural intensification decreases soil methane uptake, reducing, and even causing the loss of the methane sink function. In contrast to wetland agricultural soils (rice paddies), the methanotrophic potential in well-aerated agricultural soils have received little attention, presumably due to the anticipated low or negligible methane uptake capacity in these soils. Consequently, a detailed study verifying or refuting this assumption is still lacking. Exemplifying a typical agricultural practice, we determined the impact of bio-based residue application on soil methane flux, and determined the methanotrophic potential, including a qualitative (diagnostic microarray) and quantitative (group-specific qPCR assays) analysis of the methanotrophic community after residue amendments over 2 months. Unexpectedly, after amendments with specific residues, we detected a significant transient stimulation of methane uptake confirmed by both the methane flux measurements and methane oxidation assay. This stimulation was apparently a result of induced cell-specific activity, rather than growth of the methanotroph population. Although transient, the heightened methane uptake offsets up to 16% of total gaseous CO2 emitted during the incubation. The methanotrophic community, predominantly comprised of Methylosinus may facilitate methane oxidation in the agricultural soils. While agricultural soils are generally regarded as a net methane source or a relatively weak methane sink, our results show that methane oxidation rate can be stimulated, leading to higher soil methane uptake. Hence, even if agriculture exerts an adverse impact on soil methane uptake, implementing carefully designed management strategies (e.g. repeated application of specific residues) may compensate for the loss of the methane sink function following land-use change.

Effects of Long-Term CO2 Enrichment on Soil-Atmosphere CH4 Fluxes and the Spatial Micro-Distribution of Methanotrophic Bacteria

Background

Effects of elevated atmospheric CO₂ concentrations on plant growth and associated C cycling have intensively been studied, but less is known about effects on the fluxes of radiatively active trace gases other than CO₂. Net soil-atmosphere CH₄ fluxes are determined by the balance of soil microbially-driven methane (CH₄) oxidation and methanogenesis, and both might change under elevated CO₂.

Methods and Results

Here, we studied CH₄ dynamics in a permanent grassland exposed to elevated CO₂ for 14 years. Soil-atmosphere fluxes of CH₄ were measured using large static chambers, over a period of four years. The ecosystem was a net sink for atmospheric CH₄ for most of the time except summer to fall when net CH₄ emissions occurred. We did not detect any elevated CO₂ effects on CH₄ fluxes, but emissions were difficult to quantify due to their discontinuous nature, most likely because of ebullition from the saturated zone. Potential methanotrophic activity, determined by incubation of fresh sieved soil under standardized conditions, also did not reveal any effect of the CO₂ treatment. Finally, we determined the spatial micro-distribution of methanotrophic activity at less than 5× atmospheric (10 ppm) and elevated (10000 ppm) CH₄ concentrations, using a novel auto-radiographic technique. These analyses indicated that domains of net CH₄ assimilation were distributed throughout the analyzed top 15 cm of soils, with no dependence on CH₄ concentration or CO₂ treatment.

Conclusions

Our investigations suggest that elevated CO₂ exerts no or only minor effects on CH₄ fluxes in the type of ecosystem we studied, at least as long as soil moisture differences are small or absent as was the case here. The autoradiographic analyses further indicate that the spatial niche of CH₄ oxidation does not shift in response to CO₂ enrichment or CH₄ concentration, and that the same type of methanotrophs may oxidize CH₄ from atmospheric and soil-internal sources.

Activity and abundance of methane-oxidizing bacteria in secondary forest and manioc plantations of Amazonian Dark Earth and their adjacent soils

The oxidation of atmospheric CH₄ in upland soils is mostly mediated by uncultivated groups of microorganisms that have been identified solely by molecular markers, such as the sequence of the pmoA gene encoding the β-subunit of the particulate methane monooxygenase enzyme. The objective of this work was to compare the activity and diversity of methanotrophs in Amazonian Dark Earth soil (ADE, Hortic Anthrosol) and their adjacent non-anthropic soil. Secondly, the effect of land use in the form of manioc cultivation was examined by comparing secondary forest and plantation soils. CH₄ oxidation potentials were measured and the structure of the methanotroph communities assessed by quantitative PCR (qPCR) and amplicon pyrosequencing of pmoA genes. The oxidation potentials at low CH₄ concentrations (10 ppm of volume) were relatively high in all the secondary forest sites of both ADE and adjacent soils. CH₄ oxidation by the ADE soil only recently converted to a manioc plantation was also relatively high. In contrast, both the adjacent soils used for manioc cultivation and the ADE soil with a long history of agriculture displayed lower CH₄ uptake rates. Amplicon pyrosequencing of pmoA genes indicated that USCα, Methylocystis and the tropical upland soil cluster (TUSC) were the dominant groups depending on the site. By qPCR analysis it was found that USCα pmoA genes, which are believed to belong to atmospheric CH₄ oxidizers, were more abundant in ADE than adjacent soil. USCα pmoA genes were abundant in both forested and cultivated ADE soil, but were below the qPCR detection limit in manioc plantations of adjacent soil. The results indicate that ADE soils can harbor high abundances of atmospheric CH₄ oxidizers and are potential CH₄ sinks, but as in other upland soils this activity can be inhibited by the conversion of forest to agricultural plantations.

Sensitivity of methanotrophic community structure, abundance, and gene expression to CH4 and O2 in simulated landfill biocover soil

Pressure on mitigating CH4 emission in landfill requires better understanding of methanotrophs in landfill biocovers. Most previous studies focused on CH4 as the sole substrate. This study aims to understand the sensitivity of methanotrophs to both substrates CH4 and O2 concentrations in landfill biocovers. The estimated CH4 oxidation rates (4.66-98.7 × 10(-16) mol cell(-1) h(-1)) were evidently higher than the previous reports, suggesting that activity of methanotrophs was enhanced with both the increasing of O2 and CH4 concentrations. Denaturing gradient gel electrophoresis based on the amplification of pmoA genes suggested that methanotrophs were more sensitive to CH4 than O2. Quantification of methanotrophs using pmoA- and mmoX-targeted real-time polymerase chain reaction showed that Mbac and Mcoc as well as Mcys groups were significantly dominant. Mbac group with pmoA gene transcription was dominant. Results indicate that CH4 mitigation would have higher potential by increasing O2 at appropriate CH4 concentrations.

Methanotrophic bacteria in oilsands tailings ponds of northern Alberta

We investigated methanotrophic bacteria in slightly alkaline surface water (pH 7.4-8.7) of oilsands tailings ponds in Fort McMurray, Canada. These large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. They are primarily anoxic and produce methane but have an aerobic surface layer. Aerobic methane oxidation was measured in the surface water at rates up to 152 nmol CH4 ml(-1) water d(-1). Microbial diversity was investigated via pyrotag sequencing of amplified 16S rRNA genes, as well as by analysis of methanotroph-specific pmoA genes using both pyrosequencing and microarray analysis. The predominantly detected methanotroph in surface waters at all sampling times was an uncultured species related to the gammaproteobacterial genus Methylocaldum, although a few other methanotrophs were also detected, including Methylomonas spp. Active species were identified via (13)CH4 stable isotope probing (SIP) of DNA, combined with pyrotag sequencing and shotgun metagenomic sequencing of heavy (13)C-DNA. The SIP-PCR results demonstrated that the Methylocaldum and Methylomonas spp. actively consumed methane in fresh tailings pond water. Metagenomic analysis of DNA from the heavy SIP fraction verified the PCR-based results and identified additional pmoA genes not detected via PCR. The metagenome indicated that the overall methylotrophic community possessed known pathways for formaldehyde oxidation, carbon fixation and detoxification of nitrogenous compounds but appeared to possess only particulate methane monooxygenase not soluble methane monooxygenase.

Land application of aerobic sewage sludge does not impair methane oxidation rates of soils

The aim of this study was to measure and compare methane oxidation rates of arable and grassland soils that received 7.5t ha⁻¹ y⁻¹ of noncontaminated aerobically treated sewage sludge for ten years. Arable soils showed generally lower methane oxidation rates (from 6 to 15∗10⁻³ h⁻¹) than grassland soils (from 26 to 33∗10³ h⁻¹). Oxidation rate constants (k) of soils amended with sewage sludge were remarkably close to their respective untreated controls, but a soil, that had received a tenfold sewage sludge application (i.e. 75 t ha⁻¹ y⁻¹), showed a statistically significantly higher k-value. Laboratory addition of up to 1000 mg Pb g⁻¹ soil to this soil did not cause any significant change in methane oxidation, but caused a decrease from 13.9 to 10.9×10⁻³ h⁻¹ in the control soil. Addition of Zn was much more toxic than Pb, with a significant decrease at 300 μg g⁻¹ soil rate and an almost complete inhibition at 1500 μg g⁻¹ soil rate. Higher resistance was evident of sewage sludge treated soil in comparison to control soil, for both biomass C and CH₄ oxidation activity.

Linking activity, composition and seasonal dynamics of atmospheric methane oxidizers in a meadow soil

Microbial oxidation is the only biological sink for atmospheric methane. We assessed seasonal changes in atmospheric methane oxidation and the underlying methanotrophic communities in grassland near Giessen (Germany), along a soil moisture gradient. Soil samples were taken from the surface layer (0-10 cm) of three sites in August 2007, November 2007, February 2008 and May 2008. The sites showed seasonal differences in hydrological parameters. Net uptake rates varied seasonally between 0 and 70 μg CH(4) m(-2) h(-1). Greatest uptake rates coincided with lowest soil moisture in spring and summer. Over all sites and seasons, the methanotrophic communities were dominated by uncultivated methanotrophs. These formed a monophyletic cluster defined by the RA14, MHP and JR1 clades, referred to as upland soil cluster alphaproteobacteria (USCα)-like group. The copy numbers of pmoA genes ranged between 3.8 × 10(5)-1.9 × 10(6) copies g(-1) of soil. Temperature was positively correlated with CH(4) uptake rates (P<0.001), but had no effect on methanotrophic population dynamics. The soil moisture was negatively correlated with CH(4) uptake rates (P<0.001), but showed a positive correlation with changes in USCα-like diversity (P<0.001) and pmoA gene abundance (P<0.05). These were greatest at low net CH(4) uptake rates during winter times and coincided with an overall increase in bacterial 16S rRNA gene abundances (P<0.05). Taken together, soil moisture had a significant but opposed effect on CH(4) uptake rates and methanotrophic population dynamics, the latter being increasingly stimulated by soil moisture contents >50 vol% and primarily related to members of the MHP clade.

Real-time quantification of mcrA, pmoA for methanogen, methanotroph estimations during composting

Composting is the controlled biological decomposition of organic matter by microorganisms during predominantly aerobic conditions. It is being increasingly adopted due to its benefits in nutrient recycling, soil reclamation, and urban land use. However, it poses an environmental concern related to its contribution to greenhouse gas production. During composting, activities of methanogenic and methanotrophic communities influence the net methane (CH4) release into the atmosphere. Using quantitative polymerase chain reaction (qPCR), this study was aimed at assessing the changes in the methyl-coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) copy numbers for estimation of methanogenic and methanotrophic communities, respectively. Open-windrow composting of beef cattle (Bos Taurus L.) manure with temperatures reaching > 55 degrees C was effective indegrading commensal Escherichia coli within the first week. Quantification of community DNA revealed significant differences in mcrA and pmoA copy numbers between top and middle sections. Consistent mcrA copy numbers (7.07 to 8.69 log copy number g(-1)) were detected throughout the 15-wk composting period. However, pmoA copy number varied significantly over time, with higher values during Week 0 and 1 (6.31 and 5.41 log copy number g(-1), respectively) and the lowest at Week 11 (1.6 log copy number g(-1)). Net surface CH4 emissions over the 15-wk period were correlated with higher mcrA copy number. Higher net ratio of mrA: pmoA copy numbers was observed when surface CH4 flux was high. Our results indicate that mcrA and pmoA copy numbers vary during composting and that methanogen and methanotroph populations need to be examined in conjunction with net CH4 emissions from open-windrow composting of cattle feedlot manure.

Preferential cultivation of type II methanotrophic bacteria from littoral sediments (Lake Constance)

Most widely used medium for cultivation of methanotrophic bacteria from various environments is that proposed in 1970 by Whittenbury. In order to adapt and optimize medium for culturing of methanotrophs from freshwater sediment, media with varying concentrations of substrates, phosphate, nitrate, and other mineral salts were used to enumerate methanotrophs by the most probable number method. High concentrations (>1 mM) of magnesium and sulfate, and high concentrations of nitrate (>500 microM) significantly reduced the number of cultured methanotrophs, whereas phosphate in the range of 15-1500 microM had no influence. Also oxygen and carbon dioxide influenced the culturing efficiency, with an optimal mixing ratio of 17% O(2) and 3% CO(2); the mixing ratio of methane (6-32%) had no effect. A clone library of pmoA genes amplified by PCR from DNA extracted from sediment revealed the presence of both type I and type II methanotrophs. Nonetheless, the cultivation of methanotrophs, also with the improved medium, clearly favored growth of type II methanotrophs of the Methylosinus/Methylocystis group. Although significantly more methanotrophs could be cultured with the modified medium, their diversity did not mirror the diversity of methanotrophs in the sediment sample detected by molecular biology method.

Microbial methane oxidation processes and technologies for mitigation of landfill gas emissions

Landfill gas containing methane is produced by anaerobic degradation of organic waste. Methane is a strong greenhouse gas and landfills are one of the major anthropogenic sources of atmospheric methane. Landfill methane may be oxidized by methanotrophic microorganisms in soils or waste materials utilizing oxygen that diffuses into the cover layer from the atmosphere. The methane oxidation process, which is governed by several environmental factors, can be exploited in engineered systems developed for methane emission mitigation. Mathematical models that account for methane oxidation can be used to predict methane emissions from landfills. Additional research and technology development is needed before methane mitigation technologies utilizing microbial methane oxidation processes can become commercially viable and widely deployed.

Constraints in the colonization of natural and engineered subterranean igneous rock aquifers by aerobic methane-oxidizing bacteria inferred by culture analysis

The aerobic methane-oxidizing bacteria (MOB) are suggested to be important for the removal of oxygen from subterranean aquifers that become oxygenated by natural and engineering processes. This is primarily because MOB are ubiquitous in the environment and in addition reduce oxygen efficiently. The biogeochemical factors that will control the success of the aerobic MOB in these kinds of underground aquifers remain unknown. In this study, viable and cultivable MOB occurring at natural and engineered deep granitic aquifers targeted for the disposal of spent nuclear fuel (SNF) in the Fennoscandian Shield (approximately 3-1000 m) were enumerated. The numbers were correlated with in situ salinity, methane concentrations, conductivity, pH, and depth. A mixed population habiting freshwater aquifers (approximately 3-20 m), a potential source for the inoculation of MOB into the deeper aquifers was tested for tolerance to NaCl, temperature, pH, and an ability to produce cysts and exospores. Extrapolations show that due to changing in situ parameters (salinity, conductivity, and pH), the numbers of MOB in the aquifers dropped quickly with depth. A positive correlation between the most probable numbers of MOB and methane concentrations was observed. Furthermore, the tolerance-based tests of cultured strains indicated that the MOB in the shallow aquifers thrived best in mesophilic and neutrophilic conditions as opposed to the hyperthermophilic and alkaliphilic conditions expected to develop in an engineered subterranean SNF repository. Overall, the survival of the MOB both quantitatively and physiologically in the granitic aquifers was under the strong influence of biogeochemical factors that are strongly depth-dependent.

Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2

Methane-oxidizing bacteria (methanotrophs) attenuate methane emission from major sources, such as wetlands, rice paddies, and landfills, and constitute the only biological sink for atmospheric methane in upland soils. Their key enzyme is particulate methane monooxygenase (pMMO), which converts methane to methanol. It has long been believed that methane at the trace atmospheric mixing ratio of 1.75 parts per million by volume (ppmv) is not oxidized by the methanotrophs cultured to date, but rather only by some uncultured methanotrophs, and that type I and type II methanotrophs contain a single type of pMMO. Here, we show that the type II methanotroph Methylocystis sp. strain SC2 possesses two pMMO isozymes with different methane oxidation kinetics. The pmoCAB1 genes encoding the known type of pMMO (pMMO1) are expressed and pMMO1 oxidizes methane only at mixing ratios >600 ppmv. The pmoCAB2 genes encoding pMMO2, in contrast, are constitutively expressed, and pMMO2 oxidizes methane at lower mixing ratios, even at the trace level of atmospheric methane. Wild-type strain SC2 and mutants expressing pmoCAB2 but defective in pmoCAB1 consumed atmospheric methane for >3 months. Growth occurred at 10-100 ppmv methane. Most type II but no type I methanotrophs possess the pmoCAB2 genes. The apparent K(m) of pMMO2 (0.11 muM) in strain SC2 corresponds well with the K(m(app)) values for methane oxidation measured in soils that consume atmospheric methane, thereby explaining why these soils are dominated by type II methanotrophs, and some by Methylocystis spp., in particular. These findings change our concept of methanotroph ecology.

Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary

The surface microlayer (SML) is the thin biogenic film found at the surface of a water body. The SML is poorly understood but has been shown to be important in biogeochemical cycling and sea-air gas exchange. We sampled the SML of the Blyth estuary at two sites (salinities 21 and 31 psu) using 47 mm polycarbonate membranes. DNA was extracted from the SML and corresponding subsurface water (0.4 m depth) and microbial (bacteria and archaea) community analysis was performed using denaturing gradient gel electrophoresis of 16S rRNA gene PCR amplicons. The diversity of bacterial functional genes that encode enzyme subunits for methane monooxygenase (pmoA and mmoX) and carbon monoxide dehydrogenase (coxL) was assessed using PCR, clone library construction and restriction fragment length polymorphism (RFLP) analysis. Methanotroph genes were present only in low copy numbers and pmoA was detected only in subsurface samples. Diversity of mmoX genes was low and most of the clone sequences detected were similar to those of mmoX from Methylomonas spp. Interestingly, some sequences detected in the SML were different from those detected in the subsurface. RFLP analysis of coxL clone libraries indicated a high diversity of carbon monoxide (CO)-utilizing bacteria in the estuary. The habitats of the closely related coxL sequences suggest that CO-utilizing bacteria in the estuary are recruited from both marine and freshwater/terrestrial inputs. In contrast, methanotroph recruitment appears to occur solely from freshwater input into the estuary.

Biotic systems to mitigate landfill methane emissions

Landfill gases produced during biological degradation of buried organic wastes include methane, which when released to the atmosphere, can contribute to global climate change. Increasing use of gas collection systems has reduced the risk of escaping methane emissions entering the atmosphere, but gas capture is not 100% efficient, and further, there are still many instances when gas collection systems are not used. Biotic methane mitigation systems exploit the propensity of some naturally occurring bacteria to oxidize methane. By providing optimum conditions for microbial habitation and efficiently routing landfill gases to where they are cultivated, a number of bio-based systems, such as interim or long-term biocovers, passively or actively vented biofilters, biowindows and daily-used biotarps, have been developed that can alone, or with gas collection, mitigate landfill methane emissions. This paper reviews the science that guides bio-based designs; summarizes experiences with the diverse natural or engineered substrates used in such systems; describes some of the studies and field trials being used to evaluate them; and discusses how they can be used for better landfill operation, capping, and aftercare.

Effect of temperature on composition of the methanotrophic community in rice field and forest soil

Temperature change affects methane consumption in soil. However, there is no information on possible temperature control of methanotrophic bacterial populations. Therefore, we studied CH(4) consumption and populations of methanotrophs in an upland forest soil and a rice field soil incubated at different temperatures between 5 and 45 degrees C for up to 40 days. Potential methane consumption was measured at 4% CH(4). The temporal progress of CH(4) consumption indicated growth of methanotrophs. Both soils showed maximum CH(4) consumption at 25-35 degrees C, but no activity at >40 degrees C. In forest soil CH(4) was also consumed at 5 degrees C, but in rice soil only at 15 degrees C. Methanotroph populations were assessed by terminal restriction fragment length polymorphism (T-RFLP) targeting particulate methane monooxygenase (pmoA) genes. Eight T-RFs with relative abundance >1% were retrieved from both forest and rice soil. The individual T-RFs were tentatively assigned to different methanotrophic populations (e.g. Methylococcus/Methylocaldum, Methylomicrobium, Methylobacter, Methylocystis/Methylosinus) according to published sequence data. Two T-RFs were assigned to ammonium monooxygenase (amoA) gene sequences. Statistical tests showed that temperature affected the relative abundance of most T-RFs. Furthermore, the relative abundance of individual T-RFs differed between the two soils, and also exhibited different temperature dependence. We conclude that temperature can be an important factor regulating the community composition of methanotrophs in soil.

Abundance, distribution and potential activity of methane oxidizing bacteria in permafrost soils from the Lena Delta, Siberia

The methane oxidation potential of active layer profiles of permafrost soils from the Lena Delta, Siberia, was studied with regard to its respond to temperature, and abundance and distribution of type I and type II methanotrophs. Our results indicate vertical shifts within the optimal methane oxidation temperature and within the distribution of type I and type II methanotrophs. In the upper active layer, maximum methane oxidation potentials were detected at 21 degrees C. Deep active layer zones that are constantly exposed to temperatures below 2 degrees C showed a maximum potential to oxidize methane at 4 degrees C. Our results indicate a dominance of psychrophilic methanotrophs close to the permafrost table. Type I methanotrophs dominated throughout the active layer profiles but their number strongly fluctuated with depth. In contrast, type II methanotrophs were constantly abundant through the whole active layer and displaced type I methanotrophs close to the permafrost table. No correlation between in situ temperatures and the distribution of type I and type II methanotrophs was found. However, the distribution of type I and type II methanotrophs correlated significantly with in situ methane concentrations. Beside vertical fluctuations, the abundance of methane oxidizers also fluctuated according to different geomorphic units. Similar methanotroph cell counts were detected in samples of a flood plain and a polygon rim, whereas cell counts in samples of a polygon centre were up to 100 times lower.

Molecular characterization of methanotrophic communities in forest soils that consume atmospheric methane

Methanotroph abundance was analyzed in control and long-term nitrogen-amended pine and hardwood soils using rRNA-targeted quantitative hybridization. Family-specific 16S rRNA and pmoA/amoA genes were analyzed via PCR-directed assays to elucidate methanotrophic bacteria inhabiting soils undergoing atmospheric methane consumption. Quantitative hybridizations suggested methanotrophs related to the family Methylocystaceae were one order of magnitude more abundant than Methyloccocaceae and more sensitive to nitrogen-addition in pine soils. 16S rRNA gene phylotypes related to known Methylocystaceae and acidophilic methanotrophs and pmoA/amoA gene sequences, including three related to the upland soil cluster Alphaproteobacteria (USCalpha) group, were detected across different treatments and soil depths. Our results suggest that methanotrophic members of the Methylocystaceae and Beijerinckiaceae may be the candidates for soil atmospheric methane consumption.

Community dynamics of methanotrophic bacteria during composting of organic matter

In this study, we describe the effects of composting on the diversity, abundance and activity of the methanotrophic community present in the compost. Composting was allowed to proceed for 10 weeks in an in-vessel reactor. Self-heating capacity (Rottegrad) indicated that compost maturity was reached after 4 weeks. After 6 weeks, a second thermophilic phase was induced by manually increasing temperature to investigate whether or not the methanotrophs shifted back to the thermophilic population. Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) with primers specific for type I methanotrophs of 16S rDNA and 16S rRNA were used to characterize the composition of the microbial community. Cluster and diversity analyses of RNA DGGE patterns were more sensitive than those of DNA DGGE patterns, and revealed that mesophilic and thermophilic methanotrophic communities could be differentiated. Moreover, it was seen that the diversity of the community was low during the thermophilic phase and increased during the final maturation phase. Real-time PCR analysis was also performed on the DNA and RNA extracts and showed no changes in the abundance of type I methanotrophs during the composting process (10(9) DNA copies/g compost). However, RNA-related activity did change, with the lowest activity (10(7) cDNA copies/g compost) observed during the thermophilic phase, subsequently increasing to its maximum value (10(9) cDNA copies/g compost), and finally decreasing during the maturation phase. This study confirmed the population dynamics, as seen for general groups such as bacteria and fungi during composting, for a very specific and sensitive group of bacteria, it is the type I methanotrophs.

Estimating high-affinity methanotrophic bacterial biomass, growth, and turnover in soil by phospholipid fatty acid 13C labeling

A time series phospholipid fatty acid (PLFA) 13C-labeling study was undertaken to determine methanotrophic taxon, calculate methanotrophic biomass, and assess carbon recycling in an upland brown earth soil from Bronydd Mawr (Wales, United Kingdom). Laboratory incubations of soils were performed at ambient CH4 concentrations using synthetic air containing 2 parts per million of volume of 13CH4. Flowthrough chambers maintained a stable CH4 concentration throughout the 11-week incubation. Soils were analyzed at weekly intervals by gas chromatography (GC), GC-mass spectrometry, and GC-combustion-isotope ratio mass spectrometry to identify and quantify individual PLFAs and trace the incorporation of 13C label into the microbial biomass. Incorporation of the 13C label was seen throughout the experiment, with the rate of incorporation decreasing after 9 weeks. The delta13C values of individual PLFAs showed that 13C label was incorporated into different components to various extents and at various rates, reflecting the diversity of PLFA sources. Quantitative assessments of 13C-labeled PLFAs showed that the methanotrophic population was of constant structure throughout the experiment. The dominant 13C-labeled PLFA was 18:1omega7c, with 16:1omega5 present at lower abundance, suggesting the presence of novel type II methanotrophs. The biomass of methane-oxidizing bacteria at optimum labeling was estimated to be about 7.2 x 10(6) cells g(-1) of soil (dry weight). While recycling of 13C label from the methanotrophic biomass must occur, it is a slower process than initial 13CH4 incorporation, with only about 5 to 10% of 13C-labeled PLFAs reflecting this process. Thus, 13C-labeled PLFA distributions determined at any time point during 13CH4 incubation can be used for chemotaxonomic assessments, although extended incubations are required to achieve optimum 13C labeling for methanotrophic biomass determinations.

The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration

Methanotrophic communities were studied in several periodically water-saturated gleyic soils. When sampled, each soil had an oxic upper layer and consumed methane from the atmosphere (at 1.75 ppmv). In most gleyic soils the K(m(app)) values for methane were between 70 and 800 ppmv. These are higher than most values observed in dry upland soils, but lower than those measured in wetlands. Based on cultivation-independent retrieval of the pmoA-gene and quantification of partial pmoA gene sequences, type II (Alphaproteobacteria) methanotrophs of the genus Methylocystis spp. were abundant (> 10(7) pmoA target molecules per gram of dry soil). Type I (Gammaproteobacteria) methanotrophs related to the genera Methylobacter and Methylocaldum/Methylococcus were detected in some soils. Six pmoA sequence types not closely related to sequences from cultivated methanotrophs were detected as well, indicating that diverse uncultivated methanotrophs were present. Three Gleysols were incubated under different mixing ratios of (13)C-labelled methane to examine (13)C incorporation into phospholipid fatty acids (PLFAs). Phospholipid fatty acids typical of type II methanotrophs, 16:0 and 18:1omega7c, were labelled with (13)C in all soils after incubation under an atmosphere containing 30 ppmv of methane. Incubation under 500 ppmv of methane resulted in labelling of additional PLFAs besides 16:0 and 18:1omega7c, suggesting that the composition of the active methanotrophic community changed in response to increased methane supply. In two soils, 16:1 PLFAs typical of type I methanotrophs were strongly labelled after incubation under the high methane mixing ratio only. Type II methanotrophs are most likely responsible for atmospheric methane uptake in these soils, while type I methanotrophs become active when methane is produced in the soil.

Abundance, activity, and community structure of pelagic methane-oxidizing bacteria in temperate lakes

The abundance and activity of methane-oxidizing bacteria (MOB) in the water column were investigated in three lakes with different contents of nutrients and humic substances. The abundance of MOB was determined by analysis of group-specific phospholipid fatty acids from type I and type II MOB, and in situ activity was measured with a 14CH4 transformation method. The fatty acid analyses indicated that type I MOB most similar to species of Methylomonas, Methylomicrobium, and Methylosarcina made a substantial contribution (up to 41%) to the total bacterial biomass, whereas fatty acids from type II MOB generally had very low concentrations. The MOB biomass and oxidation activity were positively correlated and were highest in the hypo- and metalimnion during summer stratification, whereas under ice during winter, maxima occurred close to the sediments. The methanotroph biomass-specific oxidation rate (V) ranged from 0.001 to 2.77 mg CH4-C mg(-1) C day(-1) and was positively correlated with methane concentration, suggesting that methane supply largely determined the activity and biomass distribution of MOB. Our results demonstrate that type I MOB often are a large component of pelagic bacterial communities in temperate lakes. They represent a potentially important pathway for reentry of carbon and energy into pelagic food webs that would otherwise be lost as evasion of CH4.

Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea

A novel genus and species are proposed for two strains of methanotrophic bacteria isolated from hypersaline lakes in the Crimean Peninsula of Ukraine. Strains 10KiT and 4Kr are moderate halophiles that grow optimally at 1–1·5 M (5·8–8·7 %, w/v) NaCl and tolerate NaCl concentrations from 0·2 M up to 2·5 M (1·2–15 %). This optimum and upper limit are the highest for any methanotrophic bacterium known to date. The strains are Gram-negative, aerobic, non-pigmented, motile, coccoid to spindle-shaped bacteria that grow on methane or methanol only and utilize the ribulose monophosphate pathway for carbon assimilation. They are neutrophilic (growth occurs only in the range pH 6·5–7·5) and mesophilic (optimum growth occurs at 30 °C). On the basis of 16S rRNA gene sequence phylogeny, strains 10KiT and 4Kr represent a type I methanotroph within the ‘Gammaproteobacteria’. However, the 16S rRNA gene sequence displays <91·5 % identity to any public-domain sequence. The most closely related methanotrophic bacterium is the thermophilic strain HB. The DNA G+C content is 58·7 mol%. The major phospholipid fatty acids are 18 : 1ω7 (52–61 %), 16 : 0 (22–23 %) and 16 : 1ω7 (14–20 %). The dominance of 18 : 1 over 16 : 0 and 16 : 1 fatty acids is unique among known type I methanotrophs. The data suggest that strains 10KiT and 4Kr should be considered as belonging to a novel genus and species of type I methanotrophic bacteria, for which the name Methylohalobius crimeensis gen. nov., sp. nov. is proposed. Strain 10KiT (=DSM 16011T=ATCC BAA-967T) is the type strain.

Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change

We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to "RA 14" or "WB5FH-A," which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of nonsynonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors.

Community-level analysis: key genes of aerobic methane oxidation

Aerobic methane-oxidizing bacteria (methanotrophs) are a diverse group of bacteria that are currently represented by 13 recognized genera. They play a major role in the global methane cycle and are widespread in nature with representatives found in soils, freshwater, seawater, freshwater and marine sediments, peat bogs and at extremes of temperature, salinity, and pH. There has been an interest in methanotrophs for their potential in bioremediation processes. Methanotroph diversity and ecology are often studied using the "functional" genes pmoA, mmoX, and mxaF, encoding subunits of the particulate methane monooxygenase, soluble methane monooxygenase, and the methanol dehydrogenase, respectively. This chapter describes methods used to detect and analyze these functional genes.

Community structure in a methanotroph biofilter as revealed by phospholipid fatty acid analysis

The microbial community structure of two biofilters used for the oxidation of methane and organic trace gases generated in landfills was analysed by phospholipid fatty acid composition. Community structure varied with biofilter depth, reflecting varying conditions of substrate supply as well as of organic carbon content, nutrient status and osmotic stress determined by the different materials used for the individual biofilter layers. Both biofilters were dominated by type II methanotrophs. In the biofilter charged with landfill gas containing significant amounts of trace organics, fatty acid 18:1omega7c constituted 87% of the methanotrophic PLFA, while the recognised signature fatty acids 16:1omega8 and 18:1omega8, which were well represented in the other biofilter, were entirely absent. This indicates the development of a highly specific methanotrophic population, presumably as a result of the adaption to continuous organic trace gas exposure.

Impact of agricultural practices on the Zea mays L. endophytic community

Agricultural practices are known to alter bulk soil microbial communities, but little is known about the effect of such practices on the plant endophytic community. We assessed the influence of long-term applications (20 years) of herbicides and different fertilizer types on the endophytic community of maize plants grown in different field experiments. Nested PCR-denaturing gradient gel electrophoresis (DGGE) analyses targeting general bacteria, type I or II methanotrophs, actinomycetes, and general fungi were used to fingerprint the endophytic community in the roots of Zea mays L. Low intraplant variability (reproducible DGGE patterns) was observed for the bacterial, type I methanotroph, and fungal communities, whereas the patterns for endophytic actinomycetes exhibited high intraplant variability. No endophytic amplification product was obtained for type II methanotrophs. Cluster and stability analysis of the endophytic type I methanotroph patterns differentiated maize plants cultivated by using mineral fertilizer from plants cultivated by using organic fertilizer with a 100% success rate. In addition, lower methanotroph richness was observed for mineral-fertilized plants than for organically fertilized plants. The use of herbicides could not be traced by fingerprinting the endophytic type I methanotrophs or by evaluating any other endophytic microbial group. Our results indicate that the effect of agrochemicals is not limited to the bulk microbial community but also includes the root endophytic community. It is not clear if this effect is due to a direct effect on the root endophytic community or is due to changes in the bulk community, which are then reflected in the root endophytic community.

Diversity and activity of methanotrophic bacteria in different upland soils

Samples from diverse upland soils that oxidize atmospheric methane were characterized with regard to methane oxidation activity and the community composition of methanotrophic bacteria (MB). MB were identified on the basis of the detection and comparative sequence analysis of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. MB commonly detected in soils were closely related to Methylocaldum spp., Methylosinus spp., Methylocystis spp., or the "forest sequence cluster" (USC alpha), which has previously been detected in upland soils and is related to pmoA sequences of type II MB (Alphaproteobacteria). As well, a novel group of sequences distantly related (<75% derived amino acid identity) to those of known type I MB (Gammaproteobacteria) was often detected. This novel "upland soil cluster gamma" (USC gamma) was significantly more likely to be detected in soils with pH values of greater than 6.0 than in more acidic soils. To identify active MB, four selected soils were incubated with (13)CH(4) at low mixing ratios (<50 ppm of volume), and extracted methylated phospholipid fatty acids (PLFAs) were analyzed by gas chromatography-online combustion isotope ratio mass spectrometry. Incorporation of (13)C into PLFAs characteristic for methanotrophic Gammaproteobacteria was observed in all soils in which USC gamma sequences were detected, suggesting that the bacteria possessing these sequences were active methanotrophs. A pattern of labeled PLFAs typical for methanotrophic Alphaproteobacteria was obtained for a sample in which only USC alpha sequences were detected. The data indicate that different MB are present and active in different soils that oxidize atmospheric methane.