Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering

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.

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.

Responses of soil micro-eukaryotic communities to decadal drainage in a Siberian wet tussock tundra

Climate warming holds the potential to cause extensive drying of wetlands in the Arctic, but the warming-drying effects on belowground ecosystems, particularly micro-eukaryotes, remain poorly understood. We investigated the responses of soil micro-eukaryotic communities, including fungi, protists, and microbial metazoa, to decadal drainage manipulation in a Siberian wet tundra using both amplicon and shotgun metagenomic sequencing. Our results indicate that drainage treatment increased the abundance of both fungal and non-fungal micro-eukaryotic communities, with key groups such as Ascomycota (mostly order Helotiales), Nematoda, and Tardigrada being notably abundant in drained sites. Functional traits analysis showed an increase in litter saprotrophic fungi and protistan consumers, indicating their increased activities in drained sites. The effects of drainage were more pronounced in the surface soil layer than the deeper layer, as soils dry and warm from the surface. Marked compositional shifts were observed for both communities, with fungal communities being more strongly influenced by drainage-induced vegetation change than the lowered water table itself, while the vegetation effect on non-fungal micro-eukaryotes was moderate. These findings provide insights into how belowground micro-eukaryotic communities respond to the widespread drying of wetlands in the Arctic and improve our predictive understanding of future ecosystem changes.

Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine

Background

Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine.

Aims/Methods

This study aims to elucidate the archaeome structure and function in the porcine intestinal tract of healthy and H1N1 infected swine. We performed multi-omics analysis consisting of 16S rRNA gene profiling, metatranscriptomics and metaproteomics.

Results and discussion

We observed a significant increase from 0.48 to 4.50% of archaea in the intestinal tract microbiome along the ileum and colon, dominated by genera Methanobrevibacter and Methanosphaera. Furthermore, in feces of naïve and H1N1 infected swine, we observed significant but minor differences in the occurrence of archaeal phylotypes over the course of an infection experiment. Metatranscriptomic analysis of archaeal mRNAs revealed the major methanogenesis pathways of Methanobrevibacter and Methanosphaera to be hydrogenotrophic and methyl-reducing, respectively. Metaproteomics of archaeal peptides indicated some effects of the H1N1 infection on central metabolism of the gut archaea.

Conclusions/Take home message

Finally, this study provides the first multi-omics analysis and high-resolution insights into the structure and function of the porcine intestinal tract archaeome during a non-lethal Influenza A virus infection of the respiratory tract, demonstrating significant alterations in archaeal community composition and central metabolic functions.

Microbial methane cycling in sediments of Arctic thermokarst lagoons

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH₄ ) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH₄ concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, lipid biomarkers, and network analysis. We assessed how differences in geochemistry between thermokarst lakes and thermokarst lagoons, caused by the infiltration of sulfate-rich marine water, altered the microbial methane-cycling community. Anaerobic sulfate-reducing ANME-2a/2b methanotrophs dominated the sulfate-rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow and low sulfate concentrations compared to the usual marine ANME habitat. Non-competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of differences in porewater chemistry and depth. This potentially contributed to the high CH₄ concentrations observed in all sulfate-poor sediments. CH₄ concentrations in the freshwater-influenced sediments averaged 1.34 ± 0.98 μmol g^-1 , with highly depleted δ¹³ C-CH₄ values ranging from -89‰ to -70‰. In contrast, the sulfate-affected upper 300 cm of the lagoon exhibited low average CH₄ concentrations of 0.011 ± 0.005 μmol g^-1 with comparatively enriched δ¹³ C-CH₄ values of -54‰ to -37‰ pointing to substantial methane oxidation. Our study shows that lagoon formation specifically supports methane oxidizers and methane oxidation through changes in pore water chemistry, especially sulfate, while methanogens are similar to lake conditions.

Linking Transcriptional Dynamics of Peat Microbiomes to Methane Fluxes during a Summer Drought in Two Rewetted Fens

Rewetted peatlands are reestablished hot spots for CH₄ emissions, which are subject to increased drought events in the course of climate change. However, the dynamics of soil methane-cycling microbiomes in rewetted peatlands during summer drought are still poorly characterized. Using a quantitative metatranscriptomic approach, we investigated the changes in the transcript abundances of methanogen and methanotroph rRNA, as well as mcrA and pmoA mRNA before, during, and after the 2018 summer drought in a coastal and a percolation fen in northern Germany. Drought changed the community structure of methane-cycling microbiomes and decreased the CH₄ fluxes as well as the rRNA and mRNA transcript abundances of methanogens and methanotrophs, but they showed no recovery or increase after the drought ended. The rRNA transcript abundance of methanogens was not correlated with CH₄ fluxes in both fens. In the percolation fen, however, the mcrA transcript abundance showed a positive and significant correlation with CH₄ fluxes. Importantly, when integrating pmoA abundance, a stronger correlation was observed between CH₄ fluxes and mcrA/pmoA, suggesting that relationships between methanogens and methanotrophs are the key determinant of CH₄ turnover. Our study provides a comprehensive understanding of the methane-cycling microbiome feedbacks to drought events in rewetted peatlands.

Sulfur speciation in drained and restored minerotrophic peatland types of northeastern Germany

Restoring drained peatlands has been practiced to mitigate climate change, regulate water quality, and restore biodiversity. However, no information is available on the long-term impact of drainage and restoration of peatlands on total sulfur (S_t), fractions, and S species. We investigated the long-term drained and restored forested and coastal peatlands and percolation mires using the sequential S fractionation and S K-edge X-ray near-edge absorption structure (XANES) spectroscopy analysis to address this knowledge gap. The S_t concentrations in the drained forested peatland and percolation mire were low by 4 and 1.5 folds compared to their respective restored peatlands at the topsoil horizons. Similarly, the H₂O-S and NaH₂PO₄-S fractions in the drained forested peatland (28 and 18 mg kg^-1) were lower than in the restored forested peatland (165 and 166 mg kg^-1). However, the S fractions were higher in the drained percolation mire (449 and 247 mg kg^-1) than in the restored percolation mire (150 and 41 mg kg^-1). The relative proportion of the residual-S fraction (70-97% of S_t) was equivalent to the relative proportion of organic S species (76-97% of S_t) derived from the XANES analysis. The XANES analysis revealed the reduced organic S (44-62%), organic S with intermediate oxidation states (16-47%), strongly reduced (0-21%) and oxidized inorganic S species (4-12%) of the S_t. The results indicate that long-term restoration conserved S_t, decreased labile S fractions and enriched the strongly reduced inorganic and organic S species.

Linking transcriptional dynamics of CH4-cycling grassland soil microbiomes to seasonal gas fluxes

Soil CH₄ fluxes are driven by CH₄-producing and -consuming microorganisms that determine whether soils are sources or sinks of this potent greenhouse gas. To date, a comprehensive understanding of underlying microbiome dynamics has rarely been obtained in situ. Using quantitative metatranscriptomics, we aimed to link CH₄-cycling microbiomes to net surface CH₄ fluxes throughout a year in two grassland soils. CH₄ fluxes were highly dynamic: both soils were net CH₄ sources in autumn and winter and sinks in spring and summer, respectively. Correspondingly, methanogen mRNA abundances per gram soil correlated well with CH₄ fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer, when the soils acted as net CH₄ sinks. CH₄ uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. We assume that methanogen transcript abundance may be useful to approximate changes in net surface CH₄ emissions from grassland soils. High methanotroph to methanogen ratios would indicate CH₄ sink properties. Our study links for the first time the seasonal transcriptional dynamics of CH₄-cycling soil microbiomes to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.

Full Genome Sequence of a Methanomassiliicoccales Representative Enriched from Peat Soil

The full genome of a Methanomassiliicoccales strain, U3.2.1, was obtained from enrichment cultures of percolation fen peat soil under methanogenic conditions, with methanol and hydrogen as the electron acceptor and donor, respectively. Metagenomic assembly of combined long-read and short-read sequences resulted in a 1.51-Mbp circular genome.

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.

Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands

In the last decades, rewetting of drained peatlands is on the rise worldwide, to restore their significant carbon sink function. Despite the increasing understanding of peat microbiomes, little is known about the seasonal dynamics and network interactions of the microbial communities in these ecosystems, especially in rewetted fens (groundwater-fed peatlands). Here, we investigated the seasonal dynamics in both prokaryotic and eukaryotic microbiomes in three common fen types in Northern Germany. The eukaryotic microbiomes, including fungi, protists and microbial metazoa, showed significant changes in their community structures across the seasons in contrast to largely unaffected prokaryotic microbiomes. Furthermore, our results proved that the dynamics in eukaryotic microbiomes in the rewetted sites differed between fen types, specifically in terms of saprotrophs, arbuscular mycorrhiza and grazers of bacteria. The co-occurrence networks also exhibited strong seasonal dynamics that differed between rewetted and drained sites, and the correlations involving protists and prokaryotes were the major contributors to these dynamics. Our study provides the insight that microbial eukaryotes mainly define the seasonal dynamics of microbiomes in rewetted fen peatlands. Accordingly, future research should unravel the importance of eukaryotes for biogeochemical processes, especially the under-characterized protists and metazoa, in these poorly understood ecosystems.

The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?

Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5-9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized predatory bacteria affiliated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. Further, they suggest an overlooked, yet ecologically relevant food web module, independent of eukaryotic micropredators and subject to separate environmental and evolutionary pressures.

Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils

A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal amoA and 16S rRNA genes to link 16S rRNA gene classification to the novel amoA taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring amoA and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding amoA clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class Nitrososphaeria to seven different AOA (amoA) clades, including two of the most frequently detected clades (Nitrososphaerales γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. IMPORTANCE The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved amoA taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated amoA clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by amoA phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.

Short-lived peaks of stem methane emissions from mature black alder (Alnus glutinosa (L.) Gaertn.) - Irrelevant for ecosystem methane budgets?

Tree stems can be a source of the greenhouse gas methane (CH4). However, assessments of the global importance of stem CH4 emissions are complicated by a lack of research and high variability between individual ecosystems. Here, we determined the contribution of emissions from stems of mature black alder (Alnus glutinosa (L.) Gaertn.) to overall CH4 exchange in two temperate peatlands. We measured emissions from stems and soils using closed chambers in a drained and an undrained alder forest over 2 years. Furthermore, we studied the importance of alder leaves as substrate for methanogenesis in an incubation experiment. Stem CH4 emissions were short-lived and occurred only during times of inundation at the undrained site. The drained site did not show stem emissions and the soil acted as a small CH4 sink. The contribution of stem emissions to the overall CH4 budget was below 0.3% in both sites. Our results show that mature black alder can be an intermittent source of CH4 to the atmosphere. However, the low share of stem CH4 emissions in both investigated stands indicates that this pathway may be of minor relative importance in temperate peatlands, yet strongly depend on the hydrologic regime.