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

Subtle changes in topsoil microbial communities of drained forested peatlands after prolonged drought

A major consequence of anthropogenic climate change is the intensification and extension of drought periods. Prolonged drought can alter conditions in drained peatlands and cause disturbances in microbial communities in the topsoil layer of the peat. Varying environmental conditions throughout the growing season, such as the availability of organic matter and nutrients, temperature and water table, further impact these communities and consequently affect carbon and nutrient cycles. The impact of drought and new forestry practices is largely unknown in drained peatland forests. We examined how microbial communities change over a growing season in different harvesting intensities (continuous cover forestry, clear-cut and uncut) in a drained peatland site using bacterial 16S and fungal ITS2 rRNA analysis. We found seasonal differences in bacterial and fungal diversity and species richness, and subtle changes in microbial communities at the phylum and genus levels when comparing various environmental factors. Diversity, species richness and relative abundance differed in spring compared to summer and autumn. However, significant differences in the microbial community structure were not detected. Understanding the responses of microbial communities to disturbances like drought and other environmental factors provides new insights into the consequences of climate change on drained forested peatlands.

Green-house gas fluxes and soil microbial functional genes abundance in saturated and drained peatlands in South-West Iceland

The drainage of peatlands followed by land use conversion significantly impacts on the fluxes of green-house gases (GHGs, i.e. CO2, CH4, and N2O) to and from the atmosphere, driven by changes in soil properties and microbial communities. In this study, we compared saturated peatlands with drained ones used for sheep grazing or cultivated, which are common in South-West Iceland. These areas exhibit different degrees of soil saturation and nitrogen (N) content, reflecting the anthropic pressure gradient. We aimed at covering knowledge gaps about lack of estimates on N2O fluxes and drainage, by assessing the emissions of GHGs, and the impact of land conversion on these emissions. Moreover, we investigated soil microbial community functional diversity, and its connection with processes contributing to GHGs emission. GHGs emissions differed between saturated and drained peatlands, with increased soil respiration rates (CO2 emissions) and N mineralization (N2O), consistent with the trend of anthropogenic pressure. Drainage drastically reduced methane (CH4) emissions but increased CO2 emissions, resulting in a higher global warming potential (GWP). Cultivation, involving occasional tillage and fertilization, further increased N2O emissions, mediated by higher N availability and conditions favorable to nitrification. Functional genes mirrored the overall trend, showing a shift from prevalent methanogenic archaea (mcrA) in saturated peatlands to nitrifiers (amoA) in drained-cultivated areas. Environmental variables and nutrient content were critical factors affecting community composition in both environments, which overall affected the GHGs emissions and the relative contribution of the three gases.

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.

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.

Short-term responses of the soil microbiome and its environment indicate an uncertain future of restored peatland forests

Restoring peatland ecosystems involves significant uncertainty due to complex ecological and socio-economic feedbacks as well as alternative stable ecological states. The primary aim of this study was to investigate to what extent the natural functioning of drainage-affected peat soils can be restored, and to examine role of soil microbiota in this recovery process. To address these questions, a large-scale before-after-control-impact (BACI) experiment was conducted in drained peatland forests in Estonia. The restoration treatments included ditch closure and partial tree cutting to raise the water table and restore stand structure. Soil samples and environmental data were collected before and 3-4 years after the treatments; the samples were subjected to metabarcoding to assess fungal and bacterial communities and analysed for their chemical properties. The study revealed some indicators of a shift toward the reference state (natural mixotrophic bog-forests): the spatial heterogeneity in soil fungi and bacteria increased, as well as the relative abundance of saprotrophic fungi; while nitrogen content in the soil decreased significantly. However, a general stability of other physico-chemical properties (including pH remaining elevated by ca. one unit) and annual fluctuations in the microbiome suggested that soil recovery will remain incomplete and patchy for decades. The main implication is the necessity to manage hydrologically restored peatland forests while explicitly considering an uncertain future and diverse outcomes. This includes their continuous monitoring and the adoption of a precautionary approach to prevent further damage both to these ecosystems and to surrounding intact peatlands.

Peat loss collocates with a threshold in plant-mycorrhizal associations in drained peatlands encroached by trees

Drainage-induced encroachment by trees may have major effects on the carbon balance of northern peatlands, and responses of microbial communities are likely to play a central mechanistic role. We profiled the soil fungal community and estimated its genetic potential for the decay of lignin and phenolics (class II peroxidase potential) along peatland drainage gradients stretching from interior locations (undrained, open) to ditched locations (drained, forested). Mycorrhizal fungi dominated the community across the gradients. When moving towards ditches, the dominant type of mycorrhizal association abruptly shifted from ericoid mycorrhiza to ectomycorrhiza at c. 120 m from the ditches. This distance corresponded with increased peat loss, from which more than half may be attributed to oxidation. The ectomycorrhizal genus Cortinarius dominated at the drained end of the gradients and its relatively higher genetic potential to produce class II peroxidases (together with Mycena) was positively associated with peat humification and negatively with carbon-to-nitrogen ratio. Our study is consistent with a plant-soil feedback mechanism, driven by a shift in the mycorrhizal type of vegetation, that potentially mediates changes in aerobic decomposition during postdrainage succession. Such feedback may have long-term legacy effects upon postdrainage restoration efforts and implication for tree encroachment onto carbon-rich soils globally.

Variations in the archaeal community and associated methanogenesis in peat profiles of three typical peatland types in China

BACKGROUND

Peatlands contain about 500 Pg of carbon worldwide and play a dual role as both a carbon sink and an important methane (CH₄) source, thereby potentially influencing climate change. However, systematic studies on peat properties, microorganisms, methanogenesis, and their interrelations in peatlands remain limited, especially in China. Therefore, the present study aims to investigate the physicochemical properties, archaeal community, and predominant methanogenesis pathways in three typical peatlands in China, namely Hani (H), Taishanmiao (T), and Ruokeba (R) peatlands, and quantitively determine their CH₄ production potentials.

RESULTS

These peatlands exhibited high water content (WC) and total carbon content (TC), as well as low pH values. In addition, R exhibited a lower dissolved organic carbon concentration (DOC), as well as higher total iron content (TFe) and pH values compared to those observed in T. There were also clear differences in the archaeal community between the three peatlands, especially in the deep peat layers. The average relative abundance of the total methanogens ranged from 10 to 12%, of which Methanosarcinales and Methanomicrobiales were the most abundant in peat samples (8%). In contrast, Methanobacteriales were mainly distributed in the upper peat layer (0-40 cm). Besides methanogens, Marine Benthic Group D/Deep-Sea Hydrothermal Vent Euryarchaeotic Group 1 (MBG-D/DHVEG-1), Nitrosotaleales, and several other orders of Bathyarchaeota also exhibited high relative abundances, especially in T. This finding might be due to the unique geological conditions, suggesting high archaeal diversity in peatlands. In addition, the highest and lowest CH₄ production potentials were 2.38 and 0.22 μg g^-1 d^-1 in H and R, respectively. The distributions of the dominant methanogens were consistent with the respective methanogenesis pathways in the three peatlands. The pH, DOC, and WC were strongly correlated with CH₄ production potentials. However, no relationship was found between CH₄ production potential and methanogens, suggesting that CH₄ production in peatlands may not be controlled by the relative abundance of methanogens.

CONCLUSIONS

The results of the present study provide further insights into CH₄ production in peatlands in China, highlighting the importance of the archaeal community and peat physicochemical properties for studies on methanogenesis in distinct types of peatlands.

Effects of pyrogenic carbon addition after fire on soil carbon mineralization in the Great Khingan Mountains peatlands (Northeast China)

Wildfires play a critical role in regulating soil carbon (C) budgets in peatland ecosystems, and their frequency and intensity are increasing owing to climate change and human activities. Wildfires not only emit CO₂ during the combustion process but also produce pyrogenic carbon (PyC), which accumulates in the soil C pool and influences soil C decomposition. However, the role of PyC after a fire in peatland soil C mineralization has rarely been examined. This study investigated the effects of PyC addition on peatland soil C mineralization and its potential driving mechanisms using an anaerobic/aerobic incubation experiment with peat soils collected from typical peatlands in the Great Khingan Mountains, Northeast China. The effect of PyC was more pronounced under aerobic conditions than under anaerobic conditions. The mean C- mineralization rates of soil were significantly increased by 45.2 ± 15.5 % and 87.6 ± 14.3 % with 10 % PyC_250°C addition after the initial stage (D7) of aerobic and anaerobic incubation, but PyC_600°C addition caused a to decrease. Compared with PyC_600°C, PyC_250°C addition significantly increased the available N content and altered the soil microbial activities, which may be the primary reason for the increase in C mineralization rates. Furthermore, adding a high concentration of PyC (10 %) reduced the concentration of phenolics but increased phenol oxidase activity, which promoted C mineralization rates. Thus, PyC_250°C addition to peat soils mainly influences the microbial biomass C content through the accumulation of available N and phenolics, which ultimately positively affects C mineralization rates.

Responses of soil enzyme activities and bacterial community structure to different hydrological regimes during peatland restoration in the Changbai Mountain, northeast China

Appropriate hydrological management is critical for peatland restoration. An important prerequisite for peatland restoration is a recovery of soil biological processes. However, little is known about the effects of different hydrological management practices on soil biological processes during peatland restoration. In this study, the variations in soil properties, enzyme activities, and bacterial communities across different peatlands, namely natural peatland (NP), peatland restored under high water level (HR), peatland restored under alternating high-low water level (HLR), peatland restored under low water level (LR), and degraded peatland (DP), in the Changbai Mountains were investigated. Results showed that soil organic carbon, soil water content, and total nitrogen in NP were significantly higher than those in restored and degraded peatlands, and these soil properties in restored peatlands increased with the water level. The activities of soil hydrolases including β-1, 4-glucosidase, β-1, 4-n-acetylglucosidase, and acid phosphatase in NP were higher than in restored and degraded peatlands, while the activity of polyphenol oxidase in NP was the lowest. In restored peatlands, all measured enzyme activities decreased with the decline in water level. Both bacterial diversity and richness in NP were the lowest, while the highest diversity and richness were observed in HR. Redundancy analysis indicated that soil organic carbon, water level, soil water content, total nitrogen, and pH were the most important factors that affected the soil enzyme activities and bacterial community. Our findings give insight into the effects of different hydrological regimes on soil biological processes during peatland restoration. Maintaining a high water level early in the restoration process is more beneficial to restoring the ecological functions of peatlands than other hydrological regimes.

Changes in Soil Microbial Community and Carbon Flux Regime across a Subtropical Montane Peatland-to-Forest Successional Series in Taiwan

Subtropical montane peatland is among several rare ecosystems that continue to receive insufficient scientific exploration. We analyzed the vegetation types and soil bacterial composition, as well as surface carbon dioxide and methane fluxes along a successional peatland-to-upland-forest series in one such ecosystem in Taiwan. The Yuanyang Lake (YYL) study site is characterized by low temperature, high precipitation, prevailing fog, and acidic soil, which are typical conditions for the surrounding dominant Chamaecyparis obtusa var. formosana forest. Bacterial communities were dominated by Acidobacteriota and Proteobacteria. Along the bog-to-forest gradient, Proteobacteria decreased and Acidobacteriota increased while CO2 fluxes increased and CH4 fluxes decreased. Principal coordinate analysis allowed separating samples into four clusters, which correspond to samples from the bog, marsh, forest, and forest outside of the watershed. The majority of bacterial genera were found in all plots, suggesting that these communities can easily switch to other types. Variation among samples from the same vegetation type suggests influence of habitat heterogeneity on bacterial community composition. Variations of soil water content and season caused the variations of carbon fluxes. While CO2 flux decreased exponentially with increasing soil water content, the CH4 fluxes exhibited an exponential increase together with soil water content. Because YYL is in a process of gradual terrestrialization, especially under the warming climate, we expect changes in microbial composition and the greenhouse gas budget at the landscape scale within the next decades.

Carbon Dynamics in Rewetted Tropical Peat Swamp Forests

Degraded and drained peat swamp forests (PSFs) are major sources of carbon emissions in the forestry sector. Rewetting interventions aim to reduce carbon loss and to enhance the carbon stock. However, studies of rewetting interventions in tropical PSFs are still limited. This study examined the effect of rewetting interventions on carbon dynamics at a rewetted site and an undrained site. We measured aboveground carbon (AGC), belowground carbon (BGC), litterfall, heterotrophic components of soil respiration (Rh), methane emissions (CH4), and dissolved organic carbon (DOC) concentration at both sites. We found that the total carbon stock at the rewetted site was slightly lower than at the undrained site (1886.73 ± 87.69 and 2106.23 ± 214.33 Mg C ha−1, respectively). The soil organic carbon (SOC) was 1685 ± 61 Mg C ha−1 and 1912 ± 190 Mg C ha−1 at the rewetted and undrained sites, respectively, and the carbon from litterfall was 4.68 ± 0.30 and 3.92 ± 0.34 Mg C ha−1 year−1, respectively. The annual average Rh was 4.06 ± 0.02 Mg C ha−1 year−1 at the rewetted site and was 3.96 ± 0.16 Mg C ha−1 year−1 at the undrained site. In contrast, the annual average CH4 emissions were −0.0015 ± 0.00 Mg C ha−1 year−1 at the rewetted site and 0.056 ± 0.000 Mg C ha−1 year−1 at the undrained site. In the rewetted condition, carbon from litter may become stable over a longer period. Consequently, carbon loss and gain mainly depend on the magnitude of peat decomposition (Rh) and CH4 emissions.

The Effect of the Conversion from Natural Broadleaved Forests into Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) Plantations on Soil Microbial Communities and Nitrogen Functional Genes

The conversion of forests could change soil characteristics and, in turn, impact the microbial community. However, the long-term effect of forest transformation on bacterial and archaeal composition and diversity, especially on nitrogen functional communities, is poorly understood. This study aimed to explore the response of soil bacterial and archaeal communities, as well as nitrogen functional groups, to the conversion from natural broadleaved forests to Chinese fir (Cunninghamia lanceolate (Lamb.) Hook.) plantations in subtropical China by 16S rRNA amplicon sequencing. Except for soil bulk density (BD) and ammonium nitrogen (NH4+–N) content, other soil properties all decreased with the conversion from natural forests to plantations. Alpha diversity of bacteria and archaea declined with the transformation from natural forests to plantations. The composition of bacteria and archaea was significantly different between natural forests and plantations, which could be mainly attributed to the change in the content of soil organic carbon (SOC), total nitrogen (TN), nitrate nitrogen (NO3−–N), and available phosphorus (AP). The conversion of natural forests to plantations decreased the gene copies of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nifH (nitrogen fixation function) but increased denitrification gene copies (i.e., nirS, nirK, and nosZ). In summary, our study emphasizes the long-term negative effect of the conversion from natural broadleaved forests into Chinese fir plantations on the diversity and richness of soil microbial communities, thereby deeply impacting the cycling of soil nitrogen.

Dissolved organic matter concentration, molecular composition, and functional groups in contrasting management practices of peatlands

About 91,300 ha of peatlands has been rewetted in western Europe since the mid-1990s. Still, it is unknown how long-term rewetting alters the dissolved organic matter (DOM) concentration, molecular composition, and functional groups. We examined these DOM characteristics in three peatland types subjected to 47- to 231-yr drainage and 18- to 24-yr rewetting to address this knowledge gap. Cold water-extractable DOM was characterized by pyrolysis field ionization mass spectrometry (Py-FIMS) and X-ray absorption near-edge structure (XANES) spectroscopy. The dissolved organic carbon (DOC) concentration in the rewetted forest peatland was 2.7 times higher than in the drained forest peatland. However, rewetting decreased the DOC concentrations by 1.5 and 4 times in the coastal peatland and percolation mire, respectively, compared with their respective drained peatlands at the topsoil horizons. The Py-FIMS analysis revealed that all nine DOM compound classes' relative abundances differed between the rewetted and drained forest peatland with the lower relative abundances of the labile DOM compound classes in the rewetted forest peatlands. However, most DOM compound classes' relative abundances were similar between the rewetted and drained coastal peatlands and percolation mires. The XANES also revealed nine carbon and seven nitrogen functional groups with no apparent differences between the two contrasting management practices. The influence of drainage and rewetting on DOC concentration and molecular composition depends on peatland type, drainage period, rewetting intensity, and peat degradation status that should be considered in future research for understanding DOM transformation and transportation from degraded and restored peatland ecosystems.