Methane-cycling microbial communities and methane emission in natural and restored peatlands

Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture

Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.

Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective

Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.

Response of methanogenic community and their activity to temperature rise in alpine swamp meadow at different water level of the permafrost wetland on Qinghai-Tibet Plateau

Wetlands are an important source of atmospheric methane (CH₄) and are sensitive to global climate change. Alpine swamp meadows, accounting for ~50% of the natural wetlands on the Qinghai-Tibet Plateau, were considered one of the most important ecosystems. Methanogens are important functional microbes that perform the methane producing process. However, the response of methanogenic community and the main pathways of CH₄ production to temperature rise remains unknown in alpine swamp meadow at different water level in permafrost wetlands. In this study, we investigated the response of soil CH₄ production and the shift of methanogenic community to temperature rise in the alpine swamp meadow soil samples with different water levels collected from the Qinghai-Tibet Plateau through anaerobic incubation at 5°C, 15°C and 25°C. The results showed that the CH₄ contents increased with increasing incubation temperature, and were 5-10 times higher at the high water level sites (GHM1 and GHM2) than that at the low water level site (GHM3). For the high water level sites (GHM1 and GHM2), the change of incubation temperatures had little effect on the methanogenic community structure. Methanotrichaceae (32.44-65.46%), Methanobacteriaceae (19.30-58.86%) and Methanosarcinaceae (3.22-21.24%) were the dominant methanogen groups, with the abundance of Methanotrichaceae and Methanosarcinaceae having a significant positive correlation with CH₄ production (p < 0.01). For the low water level site (GHM3), the methanogenic community structure changed greatly at 25°C. The Methanobacteriaceae (59.65-77.33%) was the dominant methanogen group at 5°C and 15°C; In contrast, the Methanosarcinaceae (69.29%) dominated at 25°C, and its abundance showed a significant positive correlation with CH₄ production (p < 0.05). Collectively, these findings enhance the understanding of methanogenic community structures and CH₄ production in permafrost wetlands with different water levels during the warming process.

Integrating Decomposers, Methane-Cycling Microbes and Ecosystem Carbon Fluxes Along a Peatland Successional Gradient in a Land Uplift Region

Peatlands are carbon dioxide (CO2) sinks that, in parallel, release methane (CH4). The peatland carbon (C) balance depends on the interplay of decomposer and CH4-cycling microbes, vegetation, and environmental conditions. These interactions are susceptible to the changes that occur along a successional gradient from vascular plant-dominated systems to Sphagnum moss-dominated systems. Changes similar to this succession are predicted to occur from climate change. Here, we investigated how microbial and plant communities are interlinked with each other and with ecosystem C cycling along a successional gradient on a boreal land uplift coast. The gradient ranged from shoreline to meadows and fens, and further to bogs. Potential microbial activity (aerobic CO2 production; CH4 production and oxidation) and biomass were greatest in the early successional meadows, although their communities of aerobic decomposers (fungi, actinobacteria), methanogens, and methanotrophs did not differ from the older fens. Instead, the functional microbial communities shifted at the fen–bog transition concurrent with a sudden decrease in C fluxes. The successional patterns of decomposer versus CH4-cycling communities diverged at the bog stage, indicating strong but distinct microbial responses to Sphagnum dominance and acidity. We highlight young meadows as dynamic sites with the greatest microbial potential for C release. These hot spots of C turnover with dense sedge cover may represent a sensitive bottleneck in succession, which is necessary for eventual long-term peat accumulation. The distinctive microbes in bogs could serve as indicators of the C sink function in restoration measures that aim to stabilize the C in the peat.

Plant succession and geochemical indices in immature peatlands in the Changbai Mountains, northeastern region of China: Implications for climate change and peatland development

Peatlands cover a small portion of the Earth's land surface but hold ~30% of soil carbon (C) globally. However, few studies have focused on the early stage of peatland development, which is a key stage in the initial C sink function of peatlands. An immature peatland is vulnerable to changes in environmental conditions, e.g., temperature and water conditions, as the peat accumulation process can be easily interrupted by such changes. It is important to understand how immature peatlands develop, what conditions are beneficial to this process, and the present status of these important peatlands. Plant macrofossil analysis and geochemical characteristics of peat were used to determine the plant succession and the degree of decomposition at two peatlands developing in the Changbai Mountain region of northeastern China. The results show that during the entire plant community succession, plants in the two studied peatlands are mainly characterized by sedges (Cyperaceae) and mosses (mainly Sphagnum). Plant macrofossil analysis reveals a wetter trend in the Yuan Lake (YL) peatland in the most upper part of peat layer, which provides favorable conditions for peat accumulation and peatland development. The C/N ratios of core Chi Lake (CL) show a steady peat decomposition and accumulation process in the CL peatland. Additionally, there was a clear impact of presence of Sphagnum on the variations in the C/N ratio. In the YL peatland, macro-charcoal pieces indicated that fire events during dry hydrological conditions had great effects on biogeochemical processes within the peatland, affecting peat decomposition and the succession of the local plant community. An increase in major and trace elements suggests only weak disturbance due to the considerable distance to human settlements. This study determines the characteristics of pristine mountainous peatlands and highlights the importance of understanding the regular plant community in the early stage of peatland formation, as well as its potential effects on C sinks.

Towards a microbial process-based understanding of the resilience of peatland ecosystem service provisioning - A research agenda

Peatlands are wetland ecosystems with great significance as natural habitats and as major global carbon stores. They have been subject to widespread exploitation and degradation with resulting losses in characteristic biota and ecosystem functions such as climate regulation. More recently, large-scale programmes have been established to restore peatland ecosystems and the various services they provide to society. Despite significant progress in peatland science and restoration practice, we lack a process-based understanding of how soil microbiota influence peatland functioning and mediate the resilience and recovery of ecosystem services, to perturbations associated with land use and climate change. We argue that there is a need to: in the short-term, characterise peatland microbial communities across a range of spatial and temporal scales and develop an improved understanding of the links between peatland habitat, ecological functions and microbial processes; in the medium term, define what a successfully restored 'target' peatland microbiome looks like for key carbon cycle related ecosystem services and develop microbial-based monitoring tools for assessing restoration needs; and in the longer term, to use this knowledge to influence restoration practices and assess progress on the trajectory towards 'intact' peatland status. Rapid advances in genetic characterisation of the structure and functions of microbial communities offer the potential for transformative progress in these areas, but the scale and speed of methodological and conceptual advances in studying ecosystem functions is a challenge for peatland scientists. Advances in this area require multidisciplinary collaborations between peatland scientists, data scientists and microbiologists and ultimately, collaboration with the modelling community. Developing a process-based understanding of the resilience and recovery of peatlands to perturbations, such as climate extremes, fires, and drainage, will be key to meeting climate targets and delivering ecosystem services cost effectively.

Recovery in methanotrophic activity does not reflect on the methane-driven interaction network after peat mining

Aerobic methanotrophs are crucial in ombrotrophic peatlands, driving the methane and nitrogen cycles. Peat mining adversely affects the methanotrophs, but activity and community composition/abundances may recover after restoration. Considering that the methanotrophic activity and growth are significantly stimulated in the presence of other microorganisms, the methane-driven interaction network, encompassing methanotrophs and non-methanotrophs (i.e., methanotrophic interactome), may also be relevant in conferring community resilience. Yet, little is known of the response and recovery of the methanotrophic interactome to disturbances. Here, we determined the recovery of the methanotrophic interactome as inferred by a co-occurrence network analysis, comparing a pristine and restored peatland. We coupled a DNA-based stable isotope probing (SIP) approach using ¹³C-CH₄ to a co-occurrence network analysis derived from the ¹³C-enriched 16S rRNA gene sequences to relate the response in methanotrophic activity to the structuring of the interaction network. Methanotrophic activity and abundances recovered after peat restoration since 2000. 'Methylomonaceae' was the predominantly active methanotrophs in both peatlands, but differed in the relative abundance of Methylacidiphilaceae and Methylocystis However, bacterial community composition was distinct in both peatlands. Likewise, the methanotrophic interactome was profoundly altered in the restored peatland. Structuring of the interaction network after peat mining resulted in the loss of complexity and modularity, indicating a less connected and efficient network, which may have consequences in the event of recurring/future disturbances. Therefore, determining the response of the methane-driven interaction network, in addition to relating methanotrophic activity to community composition/abundances, provided a more comprehensive understanding of the resilience of the methanotrophs.Importance The resilience and recovery of microorganisms from disturbances are often determined with regard to their activity and community composition/abundances. Rarely has the response of the network of interacting microorganisms been considered, despite accumulating evidence showing that microbial interaction modulates community functioning. Comparing the methane-driven interaction network of a pristine and restored peatland, our findings revealed that the metabolically active microorganisms were less connected and formed less modular 'hubs' in the restored peatland, indicative of a less complex network which may have consequences with recurring disturbances and environmental changes. This also suggests that the resilience and full recovery in the methanotrophic activity and abundances do not reflect on the interaction network. Therefore, it is relevant to consider the interaction-induced response, in addition to documenting changes in activity and community composition/abundances, to provide a comprehensive understanding of the resilience of microorganisms to disturbances.

The Response of Microbial Communities to Peatland Drainage and Rewetting. A Review

Peatlands are significant global carbon stores and play an important role in mediating the flux of greenhouse gasses into the atmosphere. During the 20th century substantial areas of northern peatlands were drained to repurpose the land for industrial or agricultural use. Drained peatlands have dysfunctional microbial communities, which can lead to net carbon emissions. Rewetting of drained peatlands is therefore an environmental priority, yet our understanding of the effects of peatland drainage and rewetting on microbial communities is still incomplete. Here we summarize the last decade of research into the response of the wider microbial community, methane-cycling microorganisms, and micro-fauna to drainage and rewetting in fens and bogs in Europe and North America. Emphasis is placed on current research methodologies and their limitations. We propose targets for future work including: accounting for timescale of drainage and rewetting events; better vertical and lateral coverage of samples across a peatland; the integration of proteomic and metabolomic datasets into functional community analysis; the use of RNA sequencing to differentiate the active community from legacy DNA; and further study into the response of the viral and micro-faunal communities to peatland drainage and rewetting. This review should benefit researchers embarking on studies in wetland microbiology and non-microbiologists working on peatland drainage and rewetting in general.

Recovery of fen peatland microbiomes and predicted functional profiles after rewetting

Many of the world's peatlands have been affected by water table drawdown and subsequent loss of organic matter. Rewetting has been proposed as a measure to restore peatland functioning and to halt carbon loss, but its effectiveness is subject to debate. An important prerequisite for peatland recovery is a return of typical microbial communities, which drive key processes. To evaluate the effect of rewetting, we investigated 13 fen peatland areas across a wide (>1500 km) longitudinal gradient in Europe, in which we compared microbial communities between drained, undrained, and rewetted sites. There was a clear difference in microbial communities between drained and undrained fens, regardless of location. Community recovery upon rewetting was substantial in the majority of sites, and predictive functional profiling suggested a concomitant recovery of biogeochemical peatland functioning. However, communities in rewetted sites were only similar to those of undrained sites when soil organic matter quality (as expressed by cellulose fractions) and quantity were still sufficiently high. We estimate that a minimum organic matter content of ca. 70% is required to enable microbial recovery. We conclude that peatland recovery after rewetting is conditional on the level of drainage-induced degradation: severely altered physicochemical peat properties may preclude complete recovery for decades.

Multi-year net ecosystem carbon balance of a restored peatland reveals a return to carbon sink

Peatlands after drainage and extraction are large sources of carbon (C) to the atmosphere. Restoration, through re-wetting and revegetation, aims to return the C sink function by re-establishing conditions similar to that of an undrained peatland. However, the time needed to re-establish C sequestration is not well constrained due to the lack of multi-year measurements. We measured over 3 years the net ecosystem exchange of CO₂ (NEE), methane ( F CH 4 ), and dissolved organic carbon (DOC) at a restored post-extraction peatland (RES) in southeast Canada (restored 14 years prior to the start of the study) and compared our observations to the C balance of an intact reference peatland (REF) that has a long-term continuous flux record and is in the same climate zone. Small but significant differences in winter respiration driven by temperature were mainly responsible for differences in cumulative NEE between years. Low growing season inter-annual variability was linked to constancy of the initial spring water table position, controlled by the blocked drainage ditches and the presence of water storage structures (bunds and pools). Half-hour F CH 4 at RES was small except when Typha latifolia-invaded drainage ditches were in the tower footprint; this effect at the ecosystem level was small as ditches represent a minor fraction of RES. The restored peatland was an annual sink for CO₂ (-90 ± 18 g C m^-2  year^-1 ), a source of CH₄ (4.4 ± 0.2 g C m^-2  year^-1 ), and a source of DOC (6.9 ± 2.2 g C m^-2  year^-1 ), resulting in mean net ecosystem uptake of 78 ± 17 g C m^-2  year^-1 . Annual NEE at RES was most similar to wetter, more productive years at REF. Integrating structures to increase water retention, alongside re-establishing key species, have been effective at re-establishing the net C sink rate to that of an intact peatland.

An assessment of the potential use of compost filled plastic void forming units to serve as vents on historic landfills and related sites

Much of the solid municipal waste generated by society is sent to landfill, where biodegrading processes result in the release of methane, a major contributor to climate change. This work examined the possibility of installing a type of biofilter within paved areas of the landfill site, making use of modified pervious paving, both to allow the escape of ground gas and to avoid contamination of groundwater, using specially designed test models with provision for gas sampling in various chambers. It proposes the incorporation of an active layer within a void forming box with a view to making dual use of the pervious pavement to provide both a drainage feature and a ground gas vent, whilst providing an active layer for the oxidation of methane by microbial action. The methane removal was observed to have been effected by microbial oxidation and as such offers great promise as a method of methane removal to allow for development of landfills.

Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA-based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities.IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects.

Impact of Reed Canary Grass Cultivation and Mineral Fertilisation on the Microbial Abundance and Genetic Potential for Methane Production in Residual Peat of an Abandoned Peat Extraction Area

This study examined physiochemical conditions and prokaryotic community structure (the bacterial and archaeal 16S rRNA genes and mcrA gene abundances and proportions), and evaluated the effect of reed canary grass cultivation and mineral fertilisation on these factors, in the 60 cm thick residual peat layer of experimental plots located on an abandoned peat extraction area. The archaeal proportion was 0.67-39.56% in the prokaryotic community and the methanogens proportion was 0.01-1.77% in the archaeal community. When bacterial abundance was higher in the top 20 cm of peat, the archaea were more abundant in the 20-60 cm layer and methanogens in the 40-60 cm layer of the residual peat. The bacterial abundance was significantly increased, but archaeal abundance was not affected by cultivation. The fertiliser application had a slight effect on peat properties and on archaeal and methanogen abundances in the deeper layer of cultivated peat. The CH4 emission was positively related to mcrA abundance in the 20-60 cm of the bare peat, while in case of reed canary grass cultivation these two parameters were not correlated. Reed canary grass cultivation mitigated CH4 emission, although methanogen abundance remained approximately the same or even increased in different layers of residual peat under cultivated sites over time. This study supports the outlook of using abandoned peat extraction areas to produce reed canary grass for energy purposes as an advisable land-use practice from the perspective of atmospheric impact in peatland-rich Northern Europe.

Emissions of methane from northern peatlands: a review of management impacts and implications for future management options

Northern peatlands constitute a significant source of atmospheric methane (CH₄). However, management of undisturbed peatlands, as well as the restoration of disturbed peatlands, will alter the exchange of CH₄ with the atmosphere. The aim of this systematic review and meta‐analysis was to collate and analyze published studies to improve our understanding of the factors that control CH₄ emissions and the impacts of management on the gas flux from northern (latitude 40° to 70°N) peatlands. The analysis includes a total of 87 studies reporting measurements of CH₄ emissions taken at 186 sites covering different countries, peatland types, and management systems. Results show that CH₄ emissions from natural northern peatlands are highly variable with a 95% CI of 7.6–15.7 g C m⁻² year⁻¹ for the mean and 3.3–6.3 g C m⁻² year⁻¹ for the median. The overall annual average (mean ± SD) is 12 ± 21 g C m⁻² year⁻¹ with the highest emissions from fen ecosystems. Methane emissions from natural peatlands are mainly controlled by water table (WT) depth, plant community composition, and soil pH. Although mean annual air temperature is not a good predictor of CH₄ emissions by itself, the interaction between temperature, plant community cover, WT depth, and soil pH is important. According to short‐term forecasts of climate change, these complex interactions will be the main determinant of CH₄ emissions from northern peatlands. Drainage significantly (p < .05) reduces CH₄ emissions to the atmosphere, on average by 84%. Restoration of drained peatlands by rewetting or vegetation/rewetting increases CH₄ emissions on average by 46% compared to the original premanagement CH₄ fluxes. However, to fully evaluate the net effect of management practice on the greenhouse gas balance from high latitude peatlands, both net ecosystem exchange (NEE) and carbon exports need to be considered.

Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows

The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but to neither major changes in abundances of methane-oxidizing bacteria (MOB) nor major changes in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabeling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.

Microform-related community patterns of methane-cycling microbes in boreal Sphagnum bogs are site specific

Vegetation and water table are important regulators of methane emission in peatlands. Microform variation encompasses these factors in small-scale topographic gradients of dry hummocks, intermediate lawns and wet hollows. We examined methane production and oxidization among microforms in four boreal bogs that showed more variation of vegetation within a bog with microform than between the bogs. Potential methane production was low and differed among bogs but not consistently with microform. Methane oxidation followed water table position with microform, showing higher rates closer to surface in lawns and hollows than in hummocks. Methanogen community, analysed by mcrA terminal restriction fragment length polymorphism and dominated by Methanoregulaceae or 'Methanoflorentaceae', varied strongly with bog. The extent of microform-related variation of methanogens depended on the bog. Methanotrophs identified as Methylocystis spp. in pmoA denaturing gradient gel electrophoresis similarly showed effect of bog, and microform patterns were stronger within individual bogs. Our results suggest that methane-cycling microbes in boreal Sphagnum bogs with seemingly uniform environmental conditions may show strong site-dependent variation. The bog-intrinsic factor may be related to carbon availability but contrary to expectations appears to be unrelated to current surface vegetation, calling attention to the origin of carbon substrates for microbes in bogs.

Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands

Restored wetland soils differ significantly in physical and chemical properties from their natural counterparts even when plant community compositions are similar, but effects of restoration on microbial community composition and function are not well understood. Here, we investigate plant-microbe relationships in restored and natural tidal freshwater wetlands from two subestuaries of the Chesapeake Bay. Soil samples were collected from the root zone of Typha latifolia, Phragmites australis, Peltandra virginica, and Lythrum salicaria. Soil microbial composition was assessed using 454 pyrosequencing, and genes representing bacteria, archaea, denitrification, methanogenesis, and methane oxidation were quantified. Our analysis revealed variation in some functional gene copy numbers between plant species within sites, but intersite comparisons did not reveal consistent plant-microbe trends. We observed more microbial variations between plant species in natural wetlands, where plants have been established for a long period of time. In the largest natural wetland site, sequences putatively matching methanogens accounted for ∼17% of all sequences, and the same wetland had the highest numbers of genes coding for methane coenzyme A reductase (mcrA). Sequences putatively matching aerobic methanotrophic bacteria and anaerobic methane-oxidizing archaea (ANME) were detected in all sites, suggesting that both aerobic and anaerobic methane oxidation are possible in these systems. Our data suggest that site history and edaphic features override the influence of plant species on microbial communities in restored wetlands.

Methanotrophy induces nitrogen fixation during peatland development

Nitrogen (N) accumulation rates in peatland ecosystems indicate significant biological atmospheric N2 fixation associated with Sphagnum mosses. Here, we show that the linkage between methanotrophic carbon cycling and N2 fixation may constitute an important mechanism in the rapid accumulation of N during the primary succession of peatlands. In our experimental stable isotope enrichment study, previously overlooked methane-induced N2 fixation explained more than one-third of the new N input in the younger peatland stages, where the highest N2 fixation rates and highest methane oxidation activities co-occurred in the water-submerged moss vegetation.

Methanotrophy induces nitrogen fixation during peatland development

Nitrogen (N) accumulation rates in peatland ecosystems indicate significant biological atmospheric N2 fixation associated with Sphagnum mosses. Here, we show that the linkage between methanotrophic carbon cycling and N2 fixation may constitute an important mechanism in the rapid accumulation of N during the primary succession of peatlands. In our experimental stable isotope enrichment study, previously overlooked methane-induced N2 fixation explained more than one-third of the new N input in the younger peatland stages, where the highest N2 fixation rates and highest methane oxidation activities co-occurred in the water-submerged moss vegetation.

Identification of methanogenic archaea in the hyporheic sediment of Sitka stream

Methanogenic archaea produce methane as a metabolic product under anoxic conditions and they play a crucial role in the global methane cycle. In this study molecular diversity of methanogenic archaea in the hyporheic sediment of the lowland stream Sitka (Olomouc, Czech Republic) was analyzed by PCR amplification, cloning and sequencing analysis of the methyl coenzyme M reductase alpha subunit (mcrA) gene. Sequencing analysis of 60 clones revealed 24 different mcrA phylotypes from hyporheic sedimentary layers to a depth of 50 cm. Phylotypes were affiliated with Methanomicrobiales, Methanosarcinales and Methanobacteriales orders. Only one phylotype remains unclassified. The majority of the phylotypes showed higher affiliation with uncultured methanogens than with known methanogenic species. The presence of relatively rich assemblage of methanogenic archaea confirmed that methanogens may be an important component of hyporheic microbial communities and may affect CH₄ cycling in rivers.

Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide (CO₂) and methane (CH₄) production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between natural, mined, and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and CH₄ or CO₂ production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought about by these land uses.