Abstract. Tropical peatlands store a significant amount of carbon but are also one of the most vulnerable carbon stocks due to anthropogenic pressures and climate change. The stability and accumulation of the organic carbon stored in tropical peat systems, and its sensitivity to changing temperature and/or hydrology, is intrinsically linked to the organic matter (OM) character. However, we currently lack a detailed understanding of the OM characteristics in tropical peatlands, hindering the accurate prediction of tropical peatland stability in the 21st century. In this study, we characterise the macromolecular composition of peatland vegetation, leaf litter, and across peat depth profiles using a range of tropical (n = 7) and some temperate (n = 2) peatland ecosystems that serve as comparison. This characterisation is achieved primarily via Pyrolysis Gas Chromatography Mass Spectrometry (Py-GC-MS), complemented by Fourier-Transform Infrared Spectroscopy (FTIR). We find that silicate mineral interference in hydrologically active sites makes FTIR challenging to apply in these tropical systems. Our results also demonstrate that all sites exhibit distinct pools of putatively labile and recalcitrant (plant) OM, with both shared and distinct downcore degradation features. Most sites exhibit a downcore relative enrichment in aromatic pyrolysates, such as from lignin, vs polysaccharide pyrolysates. This relative enrichment follows a logarithmic decline, especially in the anoxic horizons. Regardless of the decomposition of the peat, however, a pyrolytic fingerprint of the original vegetation persists. This unique fingerprint is likely a driver behind the microbial community’s speciality to degrade the OM in its specific peatland, an effect known as the home advantage theory. The predicable preferential loss of polysaccharides at depth and consistent aromaticity of the leaf litter in the tropical sites can aid peatland accumulation modelling and enable more accurate predictions of peatland dynamics under future climate change.

Authigenic precipitation of clay minerals in marine sediments, termed reverse weathering, is an important process in global biogeochemical cycles due to its role in regulating alkalinity and nutrient budgets. Dissolved silicon (silicic acid) is inherently linked with reverse weathering and is a key nutrient required by a major algal group, diatoms. Previous research has suggested that diatom biogenic silica (BSi) provides an important component for reverse weathering reactions. Stable silicon isotope measurements of extracted reactive sediment 'pools' reveal that there is a strong isotopic fractionation associated with this authigenic precipitation, and are a potentially useful tool for tracing these reactions. However, previous reverse weathering studies have largely focused on tropical and subtropical deltaic environments, with less attention paid to temperate estuaries. Here, we use a two-year sediment incubation experiment with samples collected from the Severn Estuary (UK) to investigate reverse weathering processes in temperate estuary sediments. We present the first experimental constraint on silicon isotopic fractionation during the initial stage of the precipitation of amorphous authigenic phases, with fractionation factors (30 epsilon RW_authi-solution) ranging from-2.20 %o +/- 0.45 %o (1 sigma) to-4.61 %o +/- 0.47 %o (1 sigma), which is larger than previous estimates. This high degree of fractionation may help explain the strongly fractionated silicon isotope compositions observed in both reactive solid phase pools and pore fluids where reverse weathering is active. Our comparison of sterilized and non-sterilized samples demonstrates that reverse weathering type reactions can occur abiotically. However, microbial activity and the sediment mineralogy can still affect the reverse weathering type reactions, by competing for key elements in the porewaters, modulating redox cycles or promoting the rapid neoformation of authigenic phases. The use of glass beads as a substrate demonstrates that the dissolution of amorphous silica, analogous to diatom BSi, can obscure the silicon isotope fractionation signal in the porewater. These findings highlight the significant influence that biological activity and sediment composition can have on reverse weathering, offering new insights into its dynamics in different sedimentary environments.

Human degradation has caused many peatlands worldwide to shift from long-term carbon sinks to net sources. In upland blanket peatlands, erosion disrupts plant-derived carbon input and exposes deep peat, accelerating oxidation of old carbon. The efficacy of restoration in preventing carbon loss and recovering ecosystem function depends on microbial responses to both water table manipulation and renewed litter input. Yet it is unclear how these factors alter the microbial communities that ultimately control carbon storage and emissions. Here we show that microbial community composition in the eroded Waun Fignen Felen peatland, South Wales, was governed primarily by organic matter bioavailability rather than water-table position. Long-term erosion leaves a legacy of highly decomposed organic matter, unaltered by re-wetting. Where plant litter accumulation is renewed on formerly eroded peat surfaces, the influx of bioavailable organic input supports a distinct prokaryote community with a greater bacterial population size, and evidence of elevated respiration. Microbial community composition is primarily governed by the renewal of plant litter at the peat surface and utilization of recent bioavailable organic matter in the recovering layer, rather than water-table position, based on field study at Waun Fignen Felen peatland, South Wales, UK

Peatlands are vital long-term carbon sinks but also sources of trace greenhouse gases, with the balance largely governed by microbial processes. However, the structure and function of peatland microbial communities are currently poorly characterised beyond the local scale, limiting our understanding of their response to climate change. Here, we present a large-scale analysis of the peatland prokaryotic microbiome by leveraging a curated dataset of 109 publicly available metagenomes from 20 near-natural peatland sites worldwide. Despite limitations in the publicly available data, including geographic coverage and sampling depth, our analysis indicates that dominant vegetation and peatland type are the strongest predictors of peatland microbiome taxonomy and function. We show that obligate hydrogenotrophic methanogens of the family Bog-38, previously reported to be prevalent in diverse high methane-flux habitats, are abundant in northern peatlands but occur only at low abundance in tropical peatlands, suggesting a limited contribution to methane cycling in these ecosystems. In contrast to northern peatlands, the tropical peatland microbiome exhibits a broad metabolic potential for multiple key peatland biogeochemical processes, including methanogenesis and denitrification, across all depths. Intriguingly, we observe an impaired potential for complete denitrification in a significant proportion of the northern fen metagenomes, with potential implications for nitrous oxide emissions as a greenhouse gas. Overall, our study uncovers large-scale patterns and ecological drivers of the peatland prokaryotic microbiome based on existing metagenomic data, enhancing our understanding of its response to climate change and highlighting major data gaps for future research.

Iron cycling including phototrophic Fe(II) oxidation has been observed in multiple permanently stratified meromictic lakes, yet less focus has been on dimictic lakes, which seasonally overturn and are vastly more common. Here, we investigated iron cycling in a dimictic lake, Großes Heiliges Meer in northwest Germany, using 16S rRNA amplicon sequencing, as well as in-situ and lab-based experiments. Bacterial community composition in the lake follows geochemical gradients and differs markedly between oxic and anoxic conditions. Potential iron-metabolizing bacteria were found mostly in anoxic conditions at 7 and 8 m depth and were comprised of taxa from the genera Chlorobium, Thiodictyon, Sideroxydans, Geobacter, and Rhodoferrax. We were able to recreate active iron cycling (1) with an ex-situ microbial community from 8 m depth and (2) with a successful microbial enrichment culture from 7 m depth. Varying the light and organic carbon availability in lab-based experiments showed that Fe(III) reduction overshadows Fe(II) oxidation leading to a cryptic iron cycle. Overall, we could demonstrate that microbial iron cycling can be a key biogeochemical process in dimictic lakes despite regular disturbance, and that complex environmental factors such as organic substrates control the balance between Fe(II) oxidation and Fe(III) reduction.

Peatlands host the largest store of terrestrial carbon on Earth and it is widely accepted that reversal of their widespread degradation is required to meet emissions targets. Thus, significant action is underway globally to encourage their rewetting and restoration. However, restoration success can be complicated by geological factors in the local environment. Peatlands in regions with iron sulphide-rich rocks and sediments experience drastic drops in pH following drainage and release high concentrations of iron and toxic metals. Accumulation of iron and sulphur in the peat during this time will fundamentally alter biogeochemical cycling, yet we have little understanding of the extent to which these effects can be reversed following the raising of water tables. Furthermore, the long-term impacts on resident microbial communities responsible for dictating the nature and scale of green-house gas emissions from such sites is unknown.We have compared two neighbouring fens in southern England underlain by glauconite- and pyrite-rich sandstone which are within the same hydrological regime but have experienced differing degrees of historical drainage and degradation. Both fens were designated for conservation and rewetted in the 1970s. Porewater nutrient and greenhouse gas profiles, peat geochemistry, mineralogy and microbial community analyses collectively suggest lasting differences in redox state and element cycling between the two areas. Wolferton Fen, which experienced less historical land disturbance, had returned to a near-natural state in 2022. However, Dersingham Fen, which was historically deeply drained and experienced significant peat loss, had a low pH, thick crusts of iron (oxyhydr)oxides remaining on the surface, and very high porewater iron and sulphate concentrations. High abundances of these alternative terminal electron acceptors inhibit methanogens in Dersingham Fen, which continues to be a source of CO2 despite anoxia.These results suggest that iron and sulphur-rich peatlands can tolerate some degree of degradation, but extensive drainage and peat loss will likely lead to permanent contamination which remains following rewetting. However, there may be a lot to gain from restoration of such sites as rewetting can protect remaining peat and reduce CO2 emissions whilst methane production would remain low.

Peatlands are vital long-term carbon sinks but can also be greenhouse gas sources, with the balance largely governed by microbial processes. However, the structure and function of peatland microbial communities are currently poorly characterised at the global scale, limiting our understanding of their response to climate change. Here, we present a global analysis of the peatland microbiome by leveraging a dataset of 109 publicly available metagenomes from 20 near-natural peatland sites worldwide. We identify dominant vegetation and peatland type as the strongest predictors of peatland microbiome taxonomy and function. Different peatland types host distinct microbiomes, with implications for the main microbial processes in these ecosystems. We reveal a high metabolic potential of the northern bog microbiome for plant organic matter degradation, largely attributed to Acidobacteriota. Moreover, we show that the tropical peatland microbiome exhibits a broad metabolic potential for key peatland biogeochemical processes, including methanogenesis and denitrification, across all depths. Intriguingly, we observe an impaired potential for complete denitrification in a significant proportion of the northern fen metagenomes, providing implications for nitrous oxide emissions as a greenhouse gas. Overall, our study provides key insights into the global patterns and ecological drivers of the peatland microbiome, enhancing our understanding of their response to climate change. ### Competing Interest Statement The authors have declared no competing interest. UK Research and Innovation, EP/X023214/1 Natural Environment Research Council, NE/S007504/1 European Research Council, 865403

Human degradation of peatlands worldwide has turned them into net carbon sources. In upland blanket peatlands, erosion disrupts new plant-derived carbon input and exposes deep peat, putting old carbon at risk of oxidation. The efficacy of restoration in preventing carbon loss and recovering ecosystem function depends on microbial responses to both water table manipulation and renewed litter input. Yet it is unclear how these factors alter the microbial communities that ultimately control carbon storage and emissions. We show that microbial community composition in the eroded peatland of Waun Fignen Felen, South Wales, was primarily governed by the bioavailability of organic matter rather than water-table position. Long-term erosion leaves behind a legacy of highly degraded organic matter, unaltered by re-wetting. Where plant litter accumulation is renewed on formerly eroded peat surfaces, the influx of bioavailable organic input supports a distinct microbial community with greater biomass, and evidence of elevated respiration.

Global methane (CH 4 ) emissions from thawing permafrost peatlands are expected to increase substantially in the future. Net emission of CH 4 depends on the presence of more favorable terminal electron acceptors for microbial respiration, such as ferric iron (Fe(III)). In soils with high OC content, Fe(III) is often coprecipitated with organic carbon (OC). The presence of Fe(III)‐OC coprecipitates could either suppress CH 4 emissions due to inhibition of methanogenesis and stimulation of anaerobic methane oxidation coupled to Fe(III) reduction, or enhance emissions by providing additional OC. Here, we investigated the role of Fe(III)‐OC coprecipitates in net CH 4 release in a fully thawed, waterlogged permafrost peatland (Stordalen Mire, Abisko, Sweden). We synthesized Fe(III)‐OC coprecipitates using natural organic matter from the field site and added them to waterlogged soil in a microcosm experiment and in situ, and followed Fe speciation and changes in greenhouse gas emissions over time. Fe(III)‐OC coprecipitates were partially reduced (22%) within 42 days in the microcosm experiment, while almost full reduction (92 ± 4%) occurred in situ within 53 days. This led to a decrease in CH 4 emissions by 94% and 40% in the microcosm and field experiments, respectively, compared to no‐coprecipitate controls. A decrease in both RNA‐based mcrA copy numbers and relative abundance of detected methanogens indicated that methanogenesis was mainly inhibited by the addition of the coprecipitates due to microbial Fe(III) reduction. In conclusion, Fe(III)‐OC coprecipitates temporarily suppress net CH 4 emissions in fully thawed permafrost soils, and might play a similar role in mitigating CH 4 release in other (periodically) flooded soils.

Microbial mineral weathering has been predominantly investigated at shallow depths in humid and tropical environments. Much less is understood about its role in the deeper subsurface of arid and semi-arid environments where microbial weathering is limited by the availability of water and energy sources for microbial metabolism. However, the deep subsurface in these climate zones may host a microbial community that thrives on weathering of iron (Fe)-bearing minerals that serve as electron donors or acceptors. To investigate the role of microorganisms in weathering of Fe-bearing minerals in a dry climate, we recovered a >80 m deep weathering profile in a semi-arid region of the Chilean Coastal Cordillera. The bedrock is rich in Fe-bearing minerals (hornblende, biotite, chlorite, magnetite and hematite) but lacks detectable organic carbon. We evaluated the bioavailability of Fe(III)-bearing minerals that may serve as an electron acceptor for Fe(III)-reducing microorganisms. Using geochemical, mineralogical and cultivation-based methods, we found enhanced Fe bioavailability and more in vitro microbial Fe(III) reduction at increased depth. We obtained an Fe(III)-reducing enrichment culture from the deepest weathered rock found at 77 m depth. This enrichment culture is capable of reducing ferrihydrite (up to 0.6 mM d –1 ) using lactate or dihydrogen as an electron donor and grows at circumneutral pH. The main organism in the enrichment culture is the spore-forming Desulfotomaculum ruminis (abundance of 98.5%) as revealed by 16S rRNA gene amplicon sequencing. Our findings provide evidence for a microbial contribution to the weathering of Fe-bearing minerals in semi-arid environments. While microorganisms are probably not contributing to the weathering of Fe(II)-bearing silicate minerals, they are most likely of importance regarding reductive dissolution of secondary weathering products. The Fe(III) reduction quantified in this weathering profile by the in situ microbial community suggests that microorganisms are active weathering agents in semi-arid climates.

Photoferrotrophs drove primary production in the Earth's early oceans and are still abundant in modern environments. We present a draft genome sequence of a model photoferrotroph, Rhodovulum iodosum UT/N1. By comparing it with its close relative Rhodovulum robiginosum DSM 12329, we identify that these cultures were likely swapped during their history.

Significant organic nitrogen (ON) stocks have accumulated in permafrost peatlands over millennia. Climate change is expected to increase peatland thaw, making this ON more susceptible to biogeochemical degradation. However, the interplay between thaw-released N and N cycling remains poorly understood. To elucidate ON composition across a thaw transition (palsa to thaw front to bog), we employed 21 T electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and nuclear magnetic resonance (NMR) spectroscopy. In addition, we performed metatranscriptomic sequencing to evaluate microbial activity changes in N cycling pathways between the palsa and bog. We observed an approximate 10-fold increase in dissolved ON and a significant rise in ammonium concentration between the palsa and thaw front. Additionally, there was a reduction in the peptide-like fraction and an increase in the aromatic fraction of dissolved ON molecules. Dissolved ON concentrations decreased by 73 % between the thaw front and bog, while expression of ammonium-producing genes was significantly higher in the bog compared to the palsa. Our findings highlight the release and rapid compositional shift of ON during thaw transitions. This underscores the need for further studies on thaw-released N to enhance models predicting N cycling and Arctic greenhouse gas emissions.

Peatlands play a critical role in global carbon storage and methane cycling. Despite much investigation of widespread peatland initiation since the last deglaciation, the subsequent global pattern of peatland evolution and its impacts on atmospheric methane remain poorly understood. Here, we integrated palaeoecological records from >120 peatlands worldwide to develop a global synthesis of peatland evolution. Our synthesis documents peatland initiation and (fen-to-bog) transitions based on vegetation community changes, stratigraphy, and reconstructed pH variations.Our dataset reveals that peatland evolution has been continuous since ~15 ka BP (before present), with a maximum in the number of peatlands transitioning from fens to bogs during the early Holocene (10-7 ka BP). More than 50 % of peatlands completed this transition within 3,000 years of initiation, and ~75 % within 5,000 years, independent of climate state. This highlights the dominant role of autogenous peat accumulation processes in driving long-term peatland evolution. The peak in fen-bog transition coincided with a ~100 ppb decline in atmospheric methane concentrations and a ~2 ‰ depletion in methane carbon isotopes as recorded by the ice cores, possibly partly reflecting reduced methane emissions and a large-scale shift from acetoclastic to hydrogenotrophic methanogenesis due to the global fen-to-bog transitions. Supporting this, modern flux data from >130 fen and bog sites indicate that fen-bog transitions reduce methane emissions by ~50 %.In tropical peatlands, limited palaeoecological data from key regions such as the Congo Basin, Southeast Asia, and the Amazon suggest that tropical peatland evolution occurred later than that of northern peatlands, primarily during 6-2 ka BP. Unlike the herbaceous fen to Sphagnum bog transitions typical for northern peatlands, these tropical transitions were characterized by a shift from herbaceous vegetation to tree-dominated swamps, or by changes in the dominant tree species within forested swamps. Consequently, these transitions may have enhanced or at least maintained methane emissions considering that tree-mediated methane transport can be as important as sedge-mediated transport. This later tropical shift may be one of the reasons why atmospheric methane did not continue to decline during the mid-to-late Holocene.

Microbial, anoxygenic phototrophic ferrous iron (Fe(II)) oxidation (pFeOx) plays an important role in biological iron cycling. The uptake and oxidation of dissolved Fe(II) species (Fe 2+ aq ) as an electron donor for pFeOx bacteria is well understood. In contrast, the oxidation of solid Fe(II)-bearing minerals by pFeOx is less well studied, with possible mechanisms including dissolution of the minerals followed by uptake and intracellular oxidation of Fe 2+ aq or extracellular electron transfer from solid Fe(II) minerals to the bacterial cells. We investigated the oxidation of the Fe(II)-bearing carbonate mineral siderite (FeCO 3 ) by an anoxygenic phototrophic Fe(II) oxidiser Rhodopseudomonas palustris TIE-1. We aimed to explain if oxidation was controlled by chemical dissolution kinetics or whether direct electron transfer was involved. Controlled dissolution experiments using increasing dissolved bicarbonate concentrations (0–300 mM HCO 3 – ), supported by geochemical modelling, demonstrated that R. palustris TIE-1 can oxidise up to 5-fold more Fe(II) when cells are in direct contact with siderite than would be expected if oxidation occurred through dissolution alone. These results suggest that anoxygenic phototrophic Fe(II)-oxidising bacteria have the capability to enhance carbonate dissolution or even access solid-phase Fe(II) in siderite as a source of electrons, especially when siderite dissolution is limited or suppressed by geochemical constraints.

Phosphorus limits primary productivity in many (Sub-)Arctic ecosystems and may constrain biological carbon sequestration. Iron (III) oxides strongly bind phosphate in soils but can dissolve under flooded, reducing conditions induced by permafrost thaw and ground collapse. The ability for iron to regulate phosphate storage and solubility in thawing permafrost landscapes remains unclear. Here, iron-rich sediments containing iron oxides and organic-bound iron were incubated with or without added phosphate in soils along a permafrost thaw gradient to evaluate how iron-phosphate associations respond to thaw-induced redox shifts. Iron oxides partially dissolved and released sorbed phosphate when incubated in soils underlain by degraded permafrost. Iron complexed by organic matter remained stable but provided no phosphate binding capacity. Phosphate addition enhanced iron oxide dissolution and phosphorus concentrations in associated microbial biomass. Our study demonstrates that the capacity for iron oxides to immobilize and retain phosphate in permafrost peatlands decreases with permafrost thaw. Thawing of permafrost in peatlands decreases the immobilization and retention of phosphate with Fe oxides and releases initially sorbed phosphate, according to incubation experiments with Fe-rich sediments in soil along a permafrost thaw gradient.

Abstract The global iron (Fe) cycle governs important aspects of biosphere function by defining Fe availability thus supporting productivity of terrestrial and ocean ecosystems. However, the link between soil microbiome function to global patterns in terrestrial iron cycling remains poorly investigated. Here, we developed a novel database termed IRon cycle Annotation (IRcyc-A) targeted at discovering and annotating Fe cycle genes within omics data that we validated against known localized patterns of iron cycling. We leveraged this new tool to analyse the Fe cycle of over 220 publicly available soil metagenomes and metatranscriptomes encompassing a wide range of biomes on Earth. We show that the greatest abundance of Fe(III)-reduction and Fe(II)-oxidation genes were attributed to Acidobacteriota and were most abundant in the microbiomes of peatlands and iron sulfide soils, respectively. This is consistent with the high levels of dissolved Fe recorded in rivers draining such areas. In contrast, genes encoding the biosynthesis of siderophores deployed in iron sequestration in response to Fe deficiency peaked in agroecosystems with the majority assigned to Actinomycetota. Siderophore synthesis genes were negatively correlated with Fe(III)-reduction and Fe(II)-oxidation genes, supporting the view of divergent communities under low and high iron availability. Our findings highlight how iron availability shapes terrestrial microbial communities and how microbial processes can in turn contribute to global patterns in terrestrial Fe and C cycling.

Laboratory experiments show that Fe(II) oxidizing phototrophic bacteria, or photoferrotrophs, thought to be a major depositor of Archean and Palaeoproterozoic iron formations, are inhibited by toxic intermediates produced during denitrification in iron-rich systems. This identifies a previously overlooked stressor impacting mineral formation by photoferrotrophs during early Earth history.

Future permafrost thaw will likely lead to substantial release of greenhouse gases due to thawing of previously unavailable organic carbon (OC). Accurate predictions of this release are limited by poor knowledge of the bioavailability of mobilized OC during thaw. Organic carbon bioavailability decreases due to adsorption to, or coprecipitation with, poorly crystalline ferric iron (Fe(III)) (oxyhydr)oxide minerals but the maximum binding extent and binding selectivity of permafrost OC to these minerals is unknown. We therefore utilized water-extractable organic matter (WEOM) from soils across a permafrost thaw gradient to quantify adsorption and coprecipitation processes with poorly crystalline Fe(III) (oxyhydr)oxides. We found that the maximum adsorption capacity of WEOM from intact and partly thawed permafrost soils was similar (204 and 226 mg C g-1 ferrihydrite, respectively) but decreased to 81 mg C g-1 ferrihydrite for WEOM from the fully thawed site. In comparison, coprecipitation of WEOM from intact and partly thawed soils with Fe immobilized up to 925 and 1532 mg C g-1 Fe respectively due to formation of precipitated Fe(III)-OC phases. Analysis of the OC composition before and after adsorption/coprecipitation revealed that high molecular weight, oxygen-rich, carboxylic- and aromatic-rich OC was preferentially bound to Fe(III) minerals relative to low molecular weight, aliphatic-rich compounds which may be more bioavailable. This selective binding effect was stronger after adsorption than coprecipitation. Our results suggest that OC binding by Fe(III) (oxyhydr)oxides sharply decreases under fully thawed conditions and that small, aliphatic OC molecules that may be readily bioavailable are less protected across all thaw stages.