Where old meets new: An ecosystem study of methanogenesis in a reflooded agricultural peatland

Plant roots but not hydrology control microbiome composition and methane flux in temperate fen mesocosms

The rewetting of formerly drained peatlands can help to counteract climate change through the reduction of CO2 emissions. However, this can lead to resuming CH4 emissions due to changes in the microbiome, favoring CH4-producing archaea. How plants, hydrology and microbiomes interact as ultimate determinants of CH4 dynamics is still poorly understood. Using a mesocosm approach, we studied peat microbiomes, below-ground root biomass and CH4 fluxes with three different water level regimes (stable high, stable low and fluctuating) and four different plant communities (bare peat, Carex rostrata, Juncus inflexus and their mixture) over the course of one growing season. A significant difference in microbiome composition was found between mesocosms with and without plants, while the difference between plant species identity or water regimes was rather weak. A significant difference was also found between the upper and lower peat, with the difference increasing as plants grew. By the end of the growing season, the methanogen relative abundance was higher in the sub-soil layer, as well as in the bare peat and C. rostrata pots, as compared to J. inflexus or mixture pots. This was inversely linked to the larger root area of J. inflexus. The root area also negatively correlated with CH4 fluxes which positively correlated with the relative abundance of methanogens. Despite the absence or low abundance of methanotrophs in many samples, the integration of methanotroph abundance improved the quality of the correlation with CH4 fluxes, and methanogens and methanotrophs together determined CH4 fluxes in a structural equation model. However, water regime showed no significant impact on plant roots and methanogens, and consequently, on CH4 fluxes. This study showed that plant roots determined the microbiome composition and, in particular, the relative abundance of methanogens and methanotrophs, which, in interaction, drove the CH4 fluxes.

Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient

Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH4). While sulfate loading from seawater intrusion may reduce CH4 production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH4 fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH4 fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH4 fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH4 fluxes observed in oligohaline sediments.IMPORTANCELow-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.

High methane concentrations in tidal salt marsh soils: Where does the methane go?

Tidal salt marshes produce and emit CH4 . Therefore, it is critical to understand the biogeochemical controls that regulate CH4 spatial and temporal dynamics in wetlands. The prevailing paradigm assumes that acetoclastic methanogenesis is the dominant pathway for CH4 production, and higher salinity concentrations inhibit CH4 production in salt marshes. Recent evidence shows that CH4 is produced within salt marshes via methylotrophic methanogenesis, a process not inhibited by sulfate reduction. To further explore this conundrum, we performed measurements of soil-atmosphere CH4 and CO2 fluxes coupled with depth profiles of soil CH4 and CO2 pore water gas concentrations, stable and radioisotopes, pore water chemistry, and microbial community composition to assess CH4 production and fate within a temperate tidal salt marsh. We found unexpectedly high CH4 concentrations up to 145,000 μmol mol-1 positively correlated with S2- (salinity range: 6.6-14.5 ppt). Despite large CH4 production within the soil, soil-atmosphere CH4 fluxes were low but with higher emissions and extreme variability during plant senescence (84.3 ± 684.4 nmol m-2  s-1 ). CH4 and CO2 within the soil pore water were produced from young carbon, with most Δ14 C-CH4 and Δ14 C-CO2 values at or above modern. We found evidence that CH4 within soils was produced by methylotrophic and hydrogenotrophic methanogenesis. Several pathways exist after CH4 is produced, including diffusion into the atmosphere, CH4 oxidation, and lateral export to adjacent tidal creeks; the latter being the most likely dominant flux. Our findings demonstrate that CH4 production and fluxes are biogeochemically heterogeneous, with multiple processes and pathways that can co-occur and vary in importance over the year. This study highlights the potential for high CH4 production, the need to understand the underlying biogeochemical controls, and the challenges of evaluating CH4 budgets and blue carbon in salt marshes.

The unexpected long period of elevated CH4 emissions from an inundated fen meadow ended only with the occurrence of cattail (Typha latifolia)

Drainage and agricultural use transform natural peatlands from a net carbon (C) sink to a net C source. Rewetting of peatlands, despite of high methane (CH4 ) emissions, holds the potential to mitigate climate change by greatly reducing CO2 emissions. However, the time span for this transition is unknown because most studies are limited to a few years. Especially, nonpermanent open water areas often created after rewetting, are highly productive. Here, we present 14 consecutive years of CH4 flux measurements following rewetting of a formerly long-term drained peatland in the Peene valley. Measurements were made at two rewetted sites (non-inundated vs. inundated) using manual chambers. During the study period, significant differences in measured CH4 emissions occurred. In general, these differences overlapped with stages of ecosystem transition from a cultivated grassland to a polytrophic lake dominated by emergent helophytes, but could also be additionally explained by other variables. This transition started with a rapid vegetation shift from dying cultivated grasses to open water floating and submerged hydrophytes and significantly increased CH4 emissions. Since 2008, helophytes have gradually spread from the shoreline into the open water area, especially in drier years. This process was periodically delayed by exceptional inundation and eventually resulted in the inundated site being covered by emergent helophytes. While the period between 2009 and 2015 showed exceptionally high CH4 emissions, these decreased significantly after cattail and other emergent helophytes became dominant at the inundated site. Therefore, CH4 emissions declined only after 10 years of transition following rewetting, potentially reaching a new steady state. Overall, this study highlights the importance of an integrative approach to understand the shallow lakes CH4 biogeochemistry, encompassing the entire area with its mosaic of different vegetation forms. This should be ideally done through a study design including proper measurement site allocation as well as long-term measurements.

The greenhouse effect of antibiotics: The influence pathways of antibiotics on methane release from freshwater sediment

The impact of antibiotics on methane (CH₄) release from sediment involves both CH₄ production and consumption processes. However, most relevant studies lack a discussion of the pathways by which antibiotics affect CH₄ release and do not highlight the role played by the sediment chemical environment in this influence mechanism. Here, we collected field surface sediments and grouped them with various antibiotic combination concentration gradients (50, 100, 500, 1000 ng g^-1) under a 35-day indoor anaerobic constant temperature incubation. We found that the positive effect of antibiotics on sediment CH₄ release potential appeared later than the positive effect on sediment CH₄ release flux. Still, the positive effect of high-concentration antibiotics (500, 1000 ng g^-1) occurred with a lag in both processes. Also, the positive effect of high-concentration antibiotics was significantly higher than low-concentration antibiotics (50, 100 ng g^-1) in the later incubation period (p < 0.05). We performed a multi-collinearity assessment of sediment biochemical indicators, followed by a generalized linear model with negative binomial regression (GLM-NB) to obtain essential variables. In particular, we conducted the interaction analysis on CH₄ release potential and flux regression for the influence pathways construction. The partial least-squares path modeling (PLS-PM) demonstrated that the positive effect of antibiotics on CH₄ release (Total effect = 0.2579) was primarily attributed to their effect on the sediment chemical environment (Direct effect = 0.5107). These findings greatly expand our understanding of the antibiotic greenhouse effect in freshwater sediment. Further studies should more carefully consider the effects of antibiotics on the sediment chemical environment, and continuously improve the mechanistic studies of antibiotics on sediment CH₄ release.

Interactions among heavy metals and methane-metabolizing microorganisms and their effects on methane emissions in Dajiuhu peatland

Peatlands play a crucial role in mediating the emissions of methane through active biogeochemical cycling of accumulated carbon driven by methane-metabolizing microorganisms; meanwhile, they serve as vital archives of atmospheric heavy metal deposition. Despite many edaphic factors confirmed as determinants to modulate the structure of methanotrophic and methanogenic communities, recognition of interactions among them is limited. In this study, peat soils were collected from Dajiuhu peatland to assess the presence of heavy metals, and methanotrophs and methanogens were investigated via high-throughput sequencing for functional genes mcrA and pmoA. Further analyses of the correlations between methane-related functional groups were conducted. The results demonstrated that both methane-metabolizing microorganisms and heavy metals have prominent vertical heterogeneity upward and downward along the depth of 20 cm. Pb, Cd, and Hg strongly correlated with methanotrophs and methanogens across all seasons and depths, serving as forceful factors in structural variations of methanogenic and methanotrophic communities. Particularly, Pb, Cd, and Hg were identified as excessive elements in Dajiuhu peatland. Furthermore, seasonal variations of networks among methane-related functional groups and environmental factors significantly affected the changes of methane fluxes across different seasons. Concretely, the complicated interactions were detrimental to methane emissions in the Dajiuhu peatland, leading to the minimum methane emissions in winter. Our study identified the key heavy metals affecting the composition of methane-metabolizing microorganisms and linkages between seasonal variations of methane emissions and interaction among heavy metals and methane-metabolizing microorganisms, which provided much new reference and theoretical basis for integrated management of natural peatlands.

Temperature sensitivity of anaerobic methane oxidation versus methanogenesis in paddy soil: Implications for the CH4 balance under global warming

The global methane (CH₄ ) budget is based on a sensitive balance between methanogenesis and CH₄ oxidation (aerobic and anaerobic). The response of these processes to climate warming, however, is not quantified. This largely reflects our lack of knowledge about the temperature sensitivity (Q₁₀ ) of the anaerobic oxidation of CH₄ (AOM)-a ubiquitous process in soils. Based on a ¹³ CH₄ labeling experiment, we determined the rate, Q₁₀ and activation energy of AOM and of methanogenesis in a paddy soil at three temperatures (5, 20, 35°C). The rates of AOM and of methanogenesis increased exponentially with temperature, whereby the AOM rate was significantly lower than methanogenesis. Both the activation energy and Q₁₀ of AOM dropped significantly from 5-20 to 20-35°C, indicating that AOM is a highly temperature-dependent microbial process. Nonetheless, the Q₁₀ of AOM and of methanogenesis were similar at 5-35°C, implying a comparable temperature dependence of AOM and methanogenesis in paddy soil. The continuous increase of AOM Q₁₀ over the 28-day experiment reflects the successive utilization of electron acceptors according to their thermodynamic efficiency. The basic constant for Q₁₀ of AOM was calculated to be 0.1 units for each 3.2 kJ mol^-1 increase of activation energy. We estimate the AOM in paddy soils to consume 2.2~5.5 Tg CH₄ per year on a global scale. Considering these results in conjunction with literature data, the terrestrial AOM in total consumes ~30% of overall CH₄ production. Our data corroborate a similar Q₁₀ of AOM and methanogenesis. As the rate of AOM in paddy soils is lower than methanogenesis, however, it will not fully compensate for an increased methane production under climate warming.

Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential

The concentration of nitrous oxide (N₂O), an ozone-depleting greenhouse gas, is rapidly increasing in the atmosphere. Most atmospheric N₂O originates in terrestrial ecosystems, of which the majority can be attributed to microbial cycling of nitrogen in agricultural soils. Here, we demonstrate how the abundance of nitrogen cycling genes vary across intensively managed agricultural fields and adjacent restored wetlands in the Sacramento-San Joaquin Delta in California, USA. We found that the abundances of nirS and nirK genes were highest at the intensively managed organic-rich cornfield and significantly outnumber any other gene abundances, suggesting very high N₂O production potential. The quantity of nitrogen transforming genes, particularly those responsible for denitrification, nitrification and DNRA, were highest in the agricultural sites, whereas nitrogen fixation and ANAMMOX was strongly associated with the wetland sites. Although the abundance of nosZ genes was also high at the agricultural sites, the ratio of nosZ genes to nir genes was significantly higher in wetland sites indicating that these sites could act as a sink of N₂O. These findings suggest that wetland restoration could be a promising natural climate solution not only for carbon sequestration but also for reduced N₂O emissions.

Numerical Modeling of Nitrate Removal in Anoxic Groundwater during River Flooding of Riparian Zones

A numerical study demonstrates the effects of flooding on subsurface hydrological flowpaths and nitrate removal in anoxic groundwater in riparian zones with a top peat layer. A series of two-dimensional numerical simulations with changing conditions for flow (steady state or transient with flooding), hydrogeology, denitrification, and duration of flooding demonstrate how flowpaths, residence times, and nitrate removal are affected. In periods with no flooding groundwater flows horizontally and discharges to the river through the riverbed. During periods with flooding, shallow groundwater is forced upwards as discharge through peat layers that often have more optimal conditions for denitrification caused by the presence of highly reactive organic matter. The contrast in hydraulic conductivity between the sand aquifer and the overlying peat layer, as well as the flooding duration, have a significant role in determining the degree of nitrate removal.

Prompt rewetting of drained peatlands reduces climate warming despite methane emissions

Peatlands are strategic areas for climate change mitigation because of their matchless carbon stocks. Drained peatlands release this carbon to the atmosphere as carbon dioxide (CO2). Peatland rewetting effectively stops these CO2 emissions, but also re-establishes the emission of methane (CH4). Essentially, management must choose between CO2 emissions from drained, or CH4 emissions from rewetted, peatland. This choice must consider radiative effects and atmospheric lifetimes of both gases, with CO2 being a weak but persistent, and CH4 a strong but short-lived, greenhouse gas. The resulting climatic effects are, thus, strongly time-dependent. We used a radiative forcing model to compare forcing dynamics of global scenarios for future peatland management using areal data from the Global Peatland Database. Our results show that CH4 radiative forcing does not undermine the climate change mitigation potential of peatland rewetting. Instead, postponing rewetting increases the long-term warming effect through continued CO2 emissions.