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.

Ericoid mycorrhizal fungi mediate the response of ombrotrophic peatlands to fertilization: a modeling study.

Ericaceous shrubs adapt to the nutrient-poor conditions in ombrotrophic peatlands by forming symbiotic associations with ericoid mycorrhizal (ERM) fungi. Increased nutrient availability may diminish the role of ERM pathways in shrub nutrient uptake, consequently altering the biogeochemical cycling within bogs. To explore the significance of ERM fungi in ombrotrophic peatlands, we developed the model MWMmic (a peat cohort-based biogeochemical model) into MWMmic-NP by explicitly incorporating plant-soil nitrogen (N) and phosphorus (P) cycling and ERM fungi processes. The new model was applied to simulate the biogeochemical cycles in the Mer Bleue (MB) bog in Ontario, Canada, and their responses to fertilization. MWMmic_NP reproduced the carbon(C)-N-P cycles and vegetation dynamics observed in the MB bog, and their responses to fertilization. Our simulations showed that fertilization increased shrub biomass by reducing the C allocation to ERM fungi, subsequently suppressing the growth of underlying Sphagnum mosses, and decreasing the peatland C sequestration. Our species removal simulation further demonstrated that ERM fungi were key to maintaining the shrub-moss coexistence and C sink function of bogs. Our results suggest that ERM fungi play a significant role in the biogeochemical cycles in ombrotrophic peatlands and should be considered in future modeling efforts.

Variation in carbon and nitrogen concentrations among peatland categories at the global scale.

Peatlands account for 15 to 30% of the world's soil carbon (C) stock and are important controls over global nitrogen (N) cycles. However, C and N concentrations are known to vary among peatlands contributing to the uncertainty of global C inventories, but there are few global studies that relate peatland classification to peat chemistry. We analyzed 436 peat cores sampled in 24 countries across six continents and measured C, N, and organic matter (OM) content at three depths down to 70 cm. Sites were distinguished between northern (387) and tropical (49) peatlands and assigned to one of six distinct broadly recognized peatland categories that vary primarily along a pH gradient. Peat C and N concentrations, OM content, and C:N ratios differed significantly among peatland categories, but few differences in chemistry with depth were found within each category. Across all peatlands C and N concentrations in the 10-20 cm layer, were 440 ± 85.1 g kg-1 and 13.9 ± 7.4 g kg-1, with an average C:N ratio of 30.1 ± 20.8. Among peatland categories, median C concentrations were highest in bogs, poor fens and tropical swamps (446-532 g kg-1) and lowest in intermediate and extremely rich fens (375-414 g kg-1). The C:OM ratio in peat was similar across most peatland categories, except in deeper samples from ombrotrophic tropical peat swamps that were higher than other peatlands categories. Peat N concentrations and C:N ratios varied approximately two-fold among peatland categories and N concentrations tended to be higher (and C:N lower) in intermediate fens compared with other peatland types. This study reports on a unique data set and demonstrates that differences in peat C and OM concentrations among broadly classified peatland categories are predictable, which can aid future studies that use land cover assessments to refine global peatland C and N stocks.

Atmospheric nitrogen enrichment changes nutrient stoichiometry and reduces fungal N supply to peatland ericoid mycorrhizal shrubs.

Peatlands store one third of global soil carbon (C) and up to 15% of global soil nitrogen (N) but often have low plant nutrient availability owing to slow organic matter decomposition under acidic and waterlogged conditions. In rainwater-fed ombrotrophic peatlands, elevated atmospheric N deposition has increased N availability with potential consequences to ecosystem nutrient cycling. Here, we studied how 14 years of continuous N addition with either nitrate or ammonium had affected ericoid mycorrhizal (ERM) shrubs at Whim Bog, Scotland. We examined whether enrichment has influenced foliar nutrient stoichiometry and assessed using N stable isotopes whether potential changes in plant nutrient constraints are linked with plant N uptake through ERM fungi versus direct plant uptake. High doses of ammonium alleviated N deficiency in Calluna vulgaris and Erica tetralix, whereas low doses of ammonium and nitrate improved plant phosphorus (P) nutrition, indicated by the lowered foliar N:P ratios. Root acid phosphatase activities correlated positively with foliar N:P ratios, suggesting enhanced P uptake as a result of improved N nutrition. Elevated foliar δ15N of fertilized shrubs suggested that ERM fungi were less important for N supply with N fertilization. Increases in N availability in peat porewater and in direct nonmycorrhizal N uptake likely have reduced plant nitrogen uptake via mycorrhizal pathways. As the mycorrhizal N uptake correlates with the reciprocal C supply from host plants to the soil, such reduction in ERM activity may affect peat microbial communities and even accelerate C loss via decreased ERM activity and enhanced saprotrophic activity. Our results thus introduce a previously unrecognized mechanism for how anthropogenic N pollution may affect nutrient and carbon cycling within peatland ecosystems.

Quantification of Plant Root Species Composition in Peatlands Using FTIR Spectroscopy.

Evidence of plant root biomass and production in peatlands at the level of species or plant functional type (PFT) is needed for defining ecosystem functioning and predicting its future development. However, such data are limited due to methodological difficulties and the toilsomeness of separating roots from peat. We developed Fourier transform infrared (FTIR) spectroscopy based calibration models for quantifying the mass proportions of several common peatland species, and alternatively, the PFTs that these species represented, in composite root samples. We further tested whether woody roots could be classified into diameter classes, and whether dead and living roots could be separated. We aimed to solve whether general models applicable in different studies can be developed, and what would be the best way to build such models. FTIR spectra were measured from dried and powdered roots: both "pure roots", original samples of 25 species collected in the field, and "root mixtures", artificial composite samples prepared by mixing known amounts of pure roots of different species. Partial least squares regression was used to build the calibration models. The general applicability of the models was tested using roots collected in different sites or times. Our main finding is that pure roots can replace complex mixtures as calibration data. Using pure roots, we constructed generally applicable models for quantification of roots of the main PFTs of northern peatlands. The models provided accurate estimates even for far distant sites, with root mean square error (RMSE) 1.4-6.6% for graminoids, forbs and ferns. For shrubs and trees the estimates were less accurate due to higher within-species heterogeneity, partly related to variation in root diameter. Still, we obtained RMSE 3.9-10.8% for total woody roots, but up to 20.1% for different woody-root types. Species-level and dead-root models performed well within the calibration dataset but provided unacceptable estimates for independent samples, limiting their routine application in field conditions. Our PFT-level models can be applied on roots separated from soil for biomass determination or from ingrowth cores for estimating root production. We present possibilities for further development of species-level or dead-root models using the pure-root approach.

Lakes as nitrous oxide sources in the boreal landscape.

Estimates of regional and global freshwater N2 O emissions have remained inaccurate due to scarce data and complexity of the multiple processes driving N2 O fluxes the focus predominantly being on summer time measurements from emission hot spots, agricultural streams. Here, we present four-season data of N2 O concentrations in the water columns of randomly selected boreal lakes covering a large variation in latitude, lake type, area, depth, water chemistry, and land use cover. Nitrate was the key driver for N2 O dynamics, explaining as much as 78% of the variation of the seasonal mean N2 O concentrations across all lakes. Nitrate concentrations varied among seasons being highest in winter and lowest in summer. Of the surface water samples, 71% were oversaturated with N2 O relative to the atmosphere. Largest oversaturation was measured in winter and lowest in summer stressing the importance to include full year N2 O measurements in annual emission estimates. Including winter data resulted in fourfold annual N2 O emission estimates compared to summer only measurements. Nutrient-rich calcareous and large humic lakes had the highest annual N2 O emissions. Our emission estimates for Finnish and boreal lakes are 0.6 and 29 Gg N2 O-N/year, respectively. The global warming potential of N2 O from lakes cannot be neglected in the boreal landscape, being 35% of that of diffusive CH4 emission in Finnish lakes.

Long-term nutrient addition increased CH4 emission from a bog through direct and indirect effects.

Peatlands are globally significant sources of atmospheric methane (CH4). While several studies have examined the effects of nutrient addition on CH4 dynamics, there are few long-term peatland fertilization experiments, which are needed to understand the aggregated effects of nutrient deposition on ecosystem functioning. We investigated responses of CH4 flux and production to long-term field treatments with three levels of N (1.6-6.4 g m-2 yr-1 as NH4NO3), potassium and phosphorus (PK, 5.0 g P and 6.3 g K m-2 yr-1 as KH2PO4), and NPK in a temperate bog. Methane fluxes were measured in the field from May to August in 2005 and 2015. In 2015 CH4 flux was higher in the NPK treatment with 16 years of 6.4 g N m-2 yr-1 than in the control (50.5 vs. 8.6 mg CH4 m-2 d-1). The increase in CH4 flux was associated with wetter conditions derived from peat subsidence. Incubation of peat samples, with and without short-term PK amendment, showed that potential CH4 production was enhanced in the PK treatments, both from field application and by amending the incubation. We suggest that changes in this bog ecosystem originate from long-term vegetation change, increased decomposition and direct nutrient effects on microbial dynamics.

Peatland succession induces a shift in the community composition of Sphagnum-associated active methanotrophs.

Sphagnum-associated methanotrophs (SAM) are an important sink for the methane (CH4) formed in boreal peatlands. We aimed to reveal how peatland succession, which entails a directional change in several environmental variables, affects SAM and their activity. Based on the pmoA microarray results, SAM community structure changes when a peatland develops from a minerotrophic fen to an ombrotrophic bog. Methanotroph subtypes Ia, Ib, and II showed slightly contrasting patterns during succession, suggesting differences in their ecological niche adaptation. Although the direct DNA-based analysis revealed a high diversity of type Ib and II methanotrophs throughout the studied peatland chronosequence, stable isotope probing (SIP) of the pmoA gene indicated they were active mainly during the later stages of succession. In contrast, type Ia methanotrophs showed active CH4 consumption in all analyzed samples. SIP-derived (13)C-labeled 16S rRNA gene clone libraries revealed a high diversity of SAM in every succession stage including some putative Methylocella/Methyloferula methanotrophs that are not detectable with the pmoA-based approach. In addition, a high diversity of 16S rRNA gene sequences likely representing cross-labeled nonmethanotrophs was discovered, including a significant proportion of Verrucomicrobia-related sequences. These results help to predict the effects of changing environmental conditions on SAM communities and activity.

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.

Vegetation feedbacks of nutrient addition lead to a weaker carbon sink in an ombrotrophic bog.

To study vegetation feedbacks of nutrient addition on carbon sequestration capacity, we investigated vegetation and ecosystem CO2 exchange at Mer Bleue Bog, Canada in plots that had been fertilized with nitrogen (N) or with N plus phosphorus (P) and potassium (K) for 7-12 years. Gross photosynthesis, ecosystem respiration, and net CO2 exchange were measured weekly during May-September 2011 using climate-controlled chambers. A substrate-induced respiration technique was used to determine the functional ability of the microbial community. The highest N and NPK additions were associated with 40% less net CO2 uptake than the control. In the NPK additions, a diminished C sink potential was due to a 20-30% increase in ecosystem respiration, while gross photosynthesis rates did not change as greater vascular plant biomass compensated for the decrease in Sphagnum mosses. In the highest N-only treatment, small reductions in gross photosynthesis and no change in ecosystem respiration led to the reduced C sink. Substrate-induced microbial respiration was significantly higher in all levels of NPK additions compared with control. The temperature sensitivity of respiration in the plots was lower with increasing cumulative N load, suggesting more labile sources of respired CO2 . The weaker C sink potential could be explained by changes in nutrient availability, higher woody : foliar ratio, moss loss, and enhanced decomposition. Stronger responses to NPK fertilization than to N-only fertilization for both shrub biomass production and decomposition suggest that the bog ecosystem is N-P/K colimited rather than N-limited. Negative effects of further N-only deposition were indicated by delayed spring CO2 uptake. In contrast to forests, increased wood formation and surface litter accumulation in bogs seem to reduce the C sink potential owing to the loss of peat-forming Sphagnum.

Water dispersal of methanotrophic bacteria maintains functional methane oxidation in sphagnum mosses.

It is known that Sphagnum associated methanotrophy (SAM) changes in relation to the peatland water table (WT) level. After drought, rising WT is able to reactivate SAM. We aimed to reveal whether this reactivation is due to activation of indigenous methane (CH(4)) oxidizing bacteria (MOB) already present in the mosses or to MOB present in water. This was tested through two approaches: in a transplantation experiment, Sphagna lacking SAM activity were transplanted into flark water next to Sphagna oxidizing CH(4). Already after 3 days, most of the transplants showed CH(4) oxidation activity. Microarray showed that the MOB community compositions of the transplants and the original active mosses had become more similar within 28 days thus indicating MOB movement through water between mosses. Methylocystis-related type II MOB dominated the community. In a following experiment, SAM inactive mosses were bathed overnight in non-sterile and sterile-filtered SAM active site flark water. Only mosses bathed with non-sterile flark water became SAM active, which was also shown by the pmoA copy number increase of over 60 times. Thus, it was evident that MOB present in the water can colonize Sphagnum mosses. This colonization could act as a resilience mechanism for peatland CH(4) dynamics by allowing the re-emergence of CH(4) oxidation activity in Sphagnum.

The role of Sphagnum mosses in the methane cycling of a boreal mire.

Peatlands are a major natural source of atmospheric methane (CH4). Emissions from Sphagnum-dominated mires are lower than those measured from other mire types. This observation may partly be due to methanotrophic (i.e., methane-consuming) bacteria associated with Sphagnum. Twenty-three of the 41 Sphagnum species in Finland can be found in the peatland at Lakkasuo. To better understand the Sphagnum-methanotroph system, we tested the following hypotheses: (1) all these Sphagnum species support methanotrophic bacteria; (2) water level is the key environmental determinant for differences in methanotrophy across habitats; (3) under dry conditions, Sphagnum species will not host methanotrophic bacteria; and (4) methanotrophs can move from one Sphagnum shoot to another in an aquatic environment. To address hypotheses 1 and 2, we measured the water table and CH4 oxidation for all Sphagnum species at Lakkasuo in 1-5 replicates for each species. Using this systematic approach, we included Sphagnum spp. with narrow and broad ecological tolerances. To estimate the potential contribution of CH4 to moss carbon, we measured the uptake of delta13C supplied as CH4 or as carbon dioxide dissolved in water. To test hypotheses 2-4, we transplanted inactive moss patches to active sites and measured their methanotroph communities before and after transplantation. All 23 Sphagnum species showed methanotrophic activity, confirming hypothesis 1. We found that water level was the key environmental factor regulating methanotrophy in Sphagnum (hypothesis 2). Mosses that previously exhibited no CH4 oxidation became active when transplanted to an environment in which the microbes in the control mosses were actively oxidizing CH4 (hypothesis 4). Newly active transplants possessed a Methylocystis signature also found in the control Sphagnum spp. Inactive transplants also supported a Methylocystis signature in common with active transplants and control mosses, which rejects hypothesis 3. Our results imply a loose symbiosis between Sphagnum spp. and methanotrophic bacteria that accounts for potentially 10-30% of Sphagnum carbon.

Fluxes of methane, carbon dioxide and nitrous oxide in boreal lakes and potential anthropogenic effects on the aquatic greenhouse gas emissions.

We have examined how some major catchment disturbances may affect the aquatic greenhouse gas fluxes in the boreal zone, using gas flux data from studies made in 1994-1999 in the pelagic regions of seven lakes and two reservoirs in Finland. The highest pelagic seasonal average methane (CH(4)) emissions were up to 12 mmol x m(-2) x d(-1) from eutrophied lakes with agricultural catchments. Nutrient loading increases autochthonous primary production in lakes, promoting oxygen consumption and anaerobic decomposition in the sediments and this can lead to increased CH(4) release from lakes to the atmosphere. The carbon dioxide (CO(2)) fluxes were higher from reservoirs and lakes whose catchment areas were rich in peatlands or managed forests, and from eutrophied lakes in comparison to oligotrophic and mesotrophic sites. However, all these sites were net sources of CO(2) to the atmosphere. The pelagic CH(4) emissions were generally lower than those from the littoral zone. The fluxes of nitrous oxide (N(2)O) were negligible in the pelagic regions, apparently due to low nitrate inputs and/or low nitrification activity. However, the littoral zone, acting as a buffer for leached nitrogen, did release N(2)O. Anthropogenic disturbances of boreal lakes, such as increasing eutrophication, can change the aquatic greenhouse gas balance, but also the gas exchange in the littoral zone should be included in any assessment of the overall effect. It seems that autochthonous and allochthonous carbon sources, which contribute to the CH(4) and CO(2) production in lakes, also have importance in the greenhouse gas emissions from reservoirs.