Effects of short-term drying and irrigation on electron flow in mesocosms of a northern bog and an alpine fen

Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology

Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10533-024-01122-6.

Emission of greenhouse gases and soil carbon sequestration in a riparian marsh wetland in central Ohio

Wetlands are a C sink, but they also account for a large natural source of greenhouse gases (GHG), particularly methane (CH₄). Soils of wetlands play an important role in alleviating the global climate change regardless of the emission of CH₄. However, there are uncertainties about the amount of C stored and emitted from wetlands because of the site specific factors. Therefore, the present study was conducted in a temperate riverine flow-through wetland, part of which was covered with emerging macrophyte Typhus latifolia in central Ohio, USA, with the objective to assess emissions of GHGs (CH_4, CO₂, N₂O) and measure C and nitrogen (N) stocks in wetland soil in comparison to a reference upland site. The data revealed that CH₄ emission from the open and vegetated wetland ranged from 1.03-0.51 Mg C/ha/y and that of CO₂ varied from 1.26-1.51 Mg C/ha/y. In comparison, CH₄ emission from reference upland site was negligible (0.01 Mg C/ha/y), but CO₂ emission was much higher (3.24 Mg C/ha/y). The stock of C in wetland soil was 85 to 125 Mg C/ha up to 0.3 m depth. The average rate of emission was 2.15 Mg C/ha/y, but the rate of sequestration was calculated as 5.55 Mg C/ha/y. Thus, the wetland was actually a C sink. Emission of N₂O was slightly higher in vegetated wetland (0.153 mg N₂O-N/m²/h) than the open wetland and the reference site (0.129 mg N₂O-N/m²/h). Effect of temperature on emission of GHGs from the systems was also studied.

A decade of boreal rich fen greenhouse gas fluxes in response to natural and experimental water table variability

Rich fens are common boreal ecosystems with distinct hydrology, biogeochemistry and ecology that influence their carbon (C) balance. We present growing season soil chamber methane emission (F_CH4 ), ecosystem respiration (ER), net ecosystem exchange (NEE) and gross primary production (GPP) fluxes from a 9-years water table manipulation experiment in an Alaskan rich fen. The study included major flood and drought years, where wetting and drying treatments further modified the severity of droughts. Results support previous findings from peatlands that drought causes reduced magnitude of growing season F_CH4 , GPP and NEE, thus reducing or reversing their C sink function. Experimentally exacerbated droughts further reduced the capacity for the fen to act as a C sink by causing shifts in vegetation and thus reducing magnitude of maximum growing season GPP in subsequent flood years by ~15% compared to control plots. Conversely, water table position had only a weak influence on ER, but dominant contribution to ER switched from autotrophic respiration in wet years to heterotrophic in dry years. Droughts did not cause inter-annual lag effects on ER in this rich fen, as has been observed in several nutrient-poor peatlands. While ER was dependent on soil temperatures at 2 cm depth, F_CH4 was linked to soil temperatures at 25 cm. Inter-annual variability of deep soil temperatures was in turn dependent on wetness rather than air temperature, and higher F_CH4 in flooded years was thus equally due to increased methane production at depth and decreased methane oxidation near the surface. Short-term fluctuations in wetness caused significant lag effects on F_CH4 , but droughts caused no inter-annual lag effects on F_CH4 . Our results show that frequency and severity of droughts and floods can have characteristic effects on the exchange of greenhouse gases, and emphasize the need to project future hydrological regimes in rich fens.

Anaerobic trophic interactions of contrasting methane-emitting mire soils: processes versus taxa

Natural wetlands such as mires contribute up to 33% to the global emission of methane. The emission of methane is driven by trophic interactions of anaerobes that collectively degrade biopolymers. The hypothesis of this study was that these interactions in contrasting methane-emitting mire soils are functionally similar but linked to dissimilar taxa. This hypothesis was addressed by evaluating anaerobic processes and microbial taxa of eutrophic, mesotrophic and oligotrophic mire soils. Glucose was fermented to various products (e.g. H2, CO2, butyrate, acetate). Acetoclastic methanogenesis occurred, and acetogenesis and methanogenesis transformed H2-CO2 to acetate and methane, respectively. Although product profiles, cultivable cell numbers and gene copy numbers [mcrA (encodes alpha-subunit of methyl-CoM reductase) and 16S rRNA genes] were similar for all mire soils, only approximately 15% of detected family-level bacteria and species-level methanogens were shared by all mire soils. Approximately, 40% of the detected family-level taxa of each mire soil have no cultured isolates. Acidic conditions appeared to restrict the number of dominant phylotypes. The results indicated (a) that microbial processes which drive methanogenesis are similar but facilitated by dissimilar microbial communities in contrasting mire soils and (b) that mire soils harbor a large number of taxa with no cultured isolates.

Short period of oxygenation releases latch on peat decomposition

Extreme summer droughts are expected to occur more often in the future in NW Europe due to climate change. These droughts might accelerate the rate of peat oxidation in drained peat areas, with impacts on soil subsidence, GHG emission and water quality. This study aimed at providing more insight in the oxidation of deep peat layers that had not previously been exposed to air, the so-called secondary decomposition. We incubated two types of peat (eutrophic and oligotrophic), sampled from permanently anoxic peat layers from nature reserves and agricultural peat meadows. Peat samples were incubated for thirteen weeks under anoxic conditions, but were exposed to air for one to eight weeks. The production of CO2 and CH4 was quantified as a proxy for decomposition; concentrations of soluble nutrients and phenolic compounds were also measured. The results showed that oxygenation led to a steep increase in the rate of decomposition, indicated by higher carbon loss rates during and after oxygenation compared to non-oxygenated samples. Carbon loss rates increased more for eutrophic peat (agricultural area: 352%, nature reserve: 182%) than for oligotrophic peat (83% and 159% respectively). Most peat samples investigated showed higher post-oxygenation CO2 and/or CH4 production compared to the anoxic pre-oxygenation period. This indicates that oxygenation stimulates decomposition, even after anoxic conditions have returned. Contrary to the enzymic latch theory, no effects of oxygenation on the concentrations of soluble or condensed phenolic compounds were detected. Soluble nutrient concentrations did not change due to oxygenation either. Noteworthy is the occurrence of pyrite mineralization and associated acidification in eutrophic peat. Thus, low summer water levels, for example due to climate change, should be avoided in order to limit exceptionally high decomposition rates and associated problems such as increasing subsidence rates, greenhouse gas emission, sulfate release and acidification.

Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales

Understanding the dynamics of methane (CH4 ) emissions is of paramount importance because CH4 has 25 times the global warming potential of carbon dioxide (CO2 ) and is currently the second most important anthropogenic greenhouse gas. Wetlands are the single largest natural CH4 source with median emissions from published studies of 164 Tg yr(-1) , which is about a third of total global emissions. We provide a perspective on important new frontiers in obtaining a better understanding of CH4 dynamics in natural systems, with a focus on wetlands. One of the most exciting recent developments in this field is the attempt to integrate the different methodologies and spatial scales of biogeochemistry, molecular microbiology, and modeling, and thus this is a major focus of this review. Our specific objectives are to provide an up-to-date synthesis of estimates of global CH4 emissions from wetlands and other freshwater aquatic ecosystems, briefly summarize major biogeophysical controls over CH4 emissions from wetlands, suggest new frontiers in CH4 biogeochemistry, examine relationships between methanogen community structure and CH4 dynamics in situ, and to review the current generation of CH4 models. We highlight throughout some of the most pressing issues concerning global change and feedbacks on CH4 emissions from natural ecosystems. Major uncertainties in estimating current and future CH4 emissions from natural ecosystems include the following: (i) A number of important controls over CH4 production, consumption, and transport have not been, or are inadequately, incorporated into existing CH4 biogeochemistry models. (ii) Significant errors in regional and global emission estimates are derived from large spatial-scale extrapolations from highly heterogeneous and often poorly mapped wetland complexes. (iii) The limited number of observations of CH4 fluxes and their associated environmental variables loosely constrains the parameterization of process-based biogeochemistry models.

The influence of sulphate deposition on the seasonal variation of peat pore water methyl Hg in a boreal mire

In this paper we investigate the hypothesis that long-term sulphate (SO₄²⁻) deposition has made peatlands a larger source of methyl mercury (MeHg) to remote boreal lakes. This was done on experimental plots at a boreal, low sedge mire where the effect of long-term addition of SO₄²⁻ on peat pore water MeHg concentrations was observed weekly throughout the snow-free portion of 1999. The additions of SO₄²⁻ started in 1995. The seasonal mean of the pore water MeHg concentrations on the plots with 17 kg ha⁻¹ yr⁻¹ of sulphur (S) addition (1.3±0.08 ng L⁻¹, SE; n = 44) was significantly (p<0.0001) higher than the mean MeHg concentration on the plots with 3 kg ha⁻¹ yr⁻¹ of ambient S deposition (0.6±0.02 ng L⁻¹, SE; n = 44). The temporal variation in pore water MeHg concentrations during the snow free season was larger in the S-addition plots, with an amplitude of >2 ng L⁻¹ compared to +/−0.5 ng L⁻¹ in the ambient S deposition plots. The concentrations of pore water MeHg in the S-addition plots were positively correlated (r² = 0.21; p = 0.001) to the groundwater level, with the lowest concentrations of MeHg during the period with the lowest groundwater levels. The pore water MeHg concentrations were not correlated to total Hg, DOC concentration or pH. The results from this study indicate that the persistently higher pore water concentrations of MeHg in the S-addition plots are caused by the long-term additions of SO₄²⁻ to the mire surface. Since these waters are an important source of runoff, the results support the hypothesis that SO₄²⁻ deposition has increased the contribution of peatlands to MeHg in downstream aquatic systems. This would mean that the increased deposition of SO₄²⁻ in acid rain has contributed to the modern increase in the MeHg burdens of remote lakes hydrologically connected to peatlands.

Sulfate-reducing microorganisms in wetlands - fameless actors in carbon cycling and climate change

Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink. Their response to global warming and environmental pollution is one of the largest unknowns in the upcoming decades to centuries. In this review, we highlight the role of sulfate-reducing microorganisms (SRM) in the intertwined element cycles of wetlands. Although regarded primarily as methanogenic environments, biogeochemical studies have revealed a previously hidden sulfur cycle in wetlands that can sustain rapid renewal of the small standing pools of sulfate. Thus, dissimilatory sulfate reduction, which frequently occurs at rates comparable to marine surface sediments, can contribute up to 36–50% to anaerobic carbon mineralization in these ecosystems. Since sulfate reduction is thermodynamically favored relative to fermentative processes and methanogenesis, it effectively decreases gross methane production thereby mitigating the flux of methane to the atmosphere. However, very little is known about wetland SRM. Molecular analyses using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] as marker genes demonstrated that members of novel phylogenetic lineages, which are unrelated to recognized SRM, dominate dsrAB richness and, if tested, are also abundant among the dsrAB-containing wetland microbiota. These discoveries point toward the existence of so far unknown SRM that are an important part of the autochthonous wetland microbiota. In addition to these numerically dominant microorganisms, a recent stable isotope probing study of SRM in a German peatland indicated that rare biosphere members might be highly active in situ and have a considerable stake in wetland sulfate reduction. The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change.

Experimental burial inhibits methanogenesis and anaerobic decomposition in water-saturated peats

A mechanistic understanding of carbon (C) sequestration and methane (CH(4)) production is of great interest due to the importance of these processes for the global C budget. Here we demonstrate experimentally, by means of column experiments, that burial of water saturated, anoxic bog peat leads to inactivation of anaerobic respiration and methanogenesis. This effect can be related to the slowness of diffusive transport of solutes and evolving energetic constraints on anaerobic respiration. Burial lowered decomposition constants in homogenized peat sand mixtures from about 10(-5) to 10(-7) yr(-1), which is considerably slower than previously assumed, and methanogenesis slowed down in a similar manner. The latter effect could be related to acetoclastic methanogenesis approaching a minimum energy quantum of -25 kJ mol(-1) (CH(4)). Given the robustness of hydraulic properties that locate the oxic-anoxic boundary near the peatland surface and constrain solute transport deeper into the peat, this effect has likely been critical for building the peatland C store and will continue supporting long-term C sequestration in northern peatlands even under moderately changing climatic conditions.

Microorganisms with novel dissimilatory (bi)sulfite reductase genes are widespread and part of the core microbiota in low-sulfate peatlands

Peatlands of the Lehstenbach catchment (Germany) house as-yet-unidentified microorganisms with phylogenetically novel variants of the dissimilatory (bi)sulfite reductase genes dsrAB. These genes are characteristic of microorganisms that reduce sulfate, sulfite, or some organosulfonates for energy conservation but can also be present in anaerobic syntrophs. However, nothing is currently known regarding the abundance, community dynamics, and biogeography of these dsrAB-carrying microorganisms in peatlands. To tackle these issues, soils from a Lehstenbach catchment site (Schlöppnerbrunnen II fen) from different depths were sampled at three time points over a 6-year period to analyze the diversity and distribution of dsrAB-containing microorganisms by a newly developed functional gene microarray and quantitative PCR assays. Members of novel, uncultivated dsrAB lineages (approximately representing species-level groups) (i) dominated a temporally stable but spatially structured dsrAB community and (ii) represented "core" members (up to 1% to 1.7% relative abundance) of the autochthonous microbial community in this fen. In addition, denaturing gradient gel electrophoresis (DGGE)- and clone library-based comparisons of the dsrAB diversity in soils from a wet meadow, three bogs, and five fens of various geographic locations (distance of ∼1 to 400 km) identified that one Syntrophobacter-related and nine novel dsrAB lineages are widespread in low-sulfate peatlands. Signatures of biogeography in dsrB-based DGGE data were not correlated with geographic distance but could be explained largely by soil pH and wetland type, implying that the distribution of dsrAB-carrying microorganisms in wetlands on the scale of a few hundred kilometers is not limited by dispersal but determined by local environmental conditions.

Acid-tolerant microaerophilic Fe(II)-oxidizing bacteria promote Fe(III)-accumulation in a fen

The ecological importance of Fe(II)-oxidizing bacteria (FeOB) at circumneutral pH is often masked in the presence of O(2) where rapid chemical oxidation of Fe(II) predominates. This study addresses the abundance, diversity and activity of microaerophilic FeOB in an acidic fen (pH ∼ 5) located in northern Bavaria, Germany. Mean O(2) penetration depth reached 16 cm where the highest dissolved Fe(II) concentrations (up to 140 µM) were present in soil water. Acid-tolerant FeOB cultivated in gradient tubes were most abundant (10(6) cells g(-1) peat) at the 10-20 cm depth interval. A stable enrichment culture was active at up to 29% O(2) saturation and Fe(III) accumulated 1.6 times faster than in abiotic controls. An acid-tolerant, microaerophilic isolate (strain CL21) was obtained which was closely related to the neutrophilic, lithoautotrophic FeOB Sideroxydans lithotrophicus strain LD-1. CL21 oxidized Fe(II) between pH 4 and 6.0, and produced nanoscale-goethites with a clearly lower mean coherence length (7 nm) perpendicular to the (110) plane than those formed abiotically (10 nm). Our results suggest that an acid-tolerant population of FeOB is thriving at redox interfaces formed by diffusion-limited O(2) transport in acidic peatlands. Furthermore, this well-adapted population is successfully competing with chemical oxidation and thereby playing an important role in the microbial iron cycle.

A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland

Methane emission from peatlands contributes substantially to global warming but is significantly reduced by sulfate reduction, which is fuelled by globally increasing aerial sulfur pollution. However, the biology behind sulfate reduction in terrestrial ecosystems is not well understood and the key players for this process as well as their abundance remained unidentified. Comparative 16S rRNA gene stable isotope probing in the presence and absence of sulfate indicated that a Desulfosporosinus species, which constitutes only 0.006% of the total microbial community 16S rRNA genes, is an important sulfate reducer in a long-term experimental peatland field site. Parallel stable isotope probing using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] identified no additional sulfate reducers under the conditions tested. For the identified Desulfosporosinus species a high cell-specific sulfate reduction rate of up to 341 fmol SO₄²⁻ cell⁻¹ day⁻¹ was estimated. Thus, the small Desulfosporosinus population has the potential to reduce sulfate in situ at a rate of 4.0–36.8 nmol (g soil w. wt.)⁻¹ day⁻¹, sufficient to account for a considerable part of sulfate reduction in the peat soil. Modeling of sulfate diffusion to such highly active cells identified no limitation in sulfate supply even at bulk concentrations as low as 10 μM. Collectively, these data show that the identified Desulfosporosinus species, despite being a member of the ‘rare biosphere’, contributes to an important biogeochemical process that diverts the carbon flow in peatlands from methane to CO₂ and, thus, alters their contribution to global warming.