Explore the vast range of titles available.

The abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, suggesting that microbial ecology may be important in ecosystem-scale responses to global change. Microbial influence on permafrost methane release Thawing of permafrost — the frozen subsoil found in arctic and sub-arctic regions — is seen as a potential cause of soil carbon loss with accompanying emissions of the greenhouse gases methane and carbon dioxide. Carmody McCalley et al . use a natural landscape gradient of permafrost thaw in northern Sweden as a model to investigate the role of microbial communities in regulating methane cycling. They show that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, suggesting that microbial ecology can play an important role in the ecosystem-scale responses to global change. Permafrost contains about 50% of the global soil carbon 1 . It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions 2 , 3 . The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown 3 and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ 13 C signature (10–15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden 4 , 5 as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus ‘ Methanoflorens stordalenmirensis ’ 6 is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models 3 , 7 . By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.

As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems. Analysis of more than 1,500 microbial genomes sheds light on the processing of carbon released as permafrost thaws.

Carbon release due to permafrost thaw represents a potentially major positive climate change feedback. The magnitude of carbon loss and the proportion lost as methane (CH ₄) vs. carbon dioxide (CO ₂) depend on factors including temperature, mobilization of previously frozen carbon, hydrology, and changes in organic matter chemistry associated with environmental responses to thaw. While the first three of these effects are relatively well understood, the effect of organic matter chemistry remains largely unstudied. To address this gap, we examined the biogeochemistry of peat and dissolved organic matter (DOM) along a ∼40-y permafrost thaw progression from recently- to fully thawed sites in Stordalen Mire (68.35°N, 19.05°E), a thawing peat plateau in northern Sweden. Thaw-induced subsidence and the resulting inundation along this progression led to succession in vegetation types accompanied by an evolution in organic matter chemistry. Peat C/N ratios decreased whereas humification rates increased, and DOM shifted toward lower molecular weight compounds with lower aromaticity, lower organic oxygen content, and more abundant microbially produced compounds. Corresponding changes in decomposition along this gradient included increasing CH ₄ and CO ₂ production potentials, higher relative CH ₄/CO ₂ ratios, and a shift in CH ₄ production pathway from CO ₂ reduction to acetate cleavage. These results imply that subsidence and thermokarst-associated increases in organic matter lability cause shifts in biogeochemical processes toward faster decomposition with an increasing proportion of carbon released as CH ₄. This impact of permafrost thaw on organic matter chemistry could intensify the predicted climate feedbacks of increasing temperatures, permafrost carbon mobilization, and hydrologic changes.

Peatlands represent large terrestrial carbon banks. Given that most peat accumulates in boreal regions, where low temperatures and water saturation preserve organic matter, the existence of peat in (sub)tropical regions remains enigmatic. Here we examined peat and plant chemistry across a latitudinal transect from the Arctic to the tropics. Near-surface low-latitude peat has lower carbohydrate and greater aromatic content than near-surface high-latitude peat, creating a reduced oxidation state and resulting recalcitrance. This recalcitrance allows peat to persist in the (sub)tropics despite warm temperatures. Because we observed similar declines in carbohydrate content with depth in high-latitude peat, our data explain recent field-scale deep peat warming experiments in which catotelm (deeper) peat remained stable despite temperature increases up to 9 °C. We suggest that high-latitude deep peat reservoirs may be stabilized in the face of climate change by their ultimately lower carbohydrate and higher aromatic composition, similar to tropical peats. Large peatlands exist at high latitudes because flooded conditions and cold temperatures slow decomposition, so the presence of (sub)tropical peat is enigmatic. Here the authors show that low-latitude peat is preserved due to lower carbohydrate and greater aromatic content resulting in chemical recalcitrance.

We employed two compelling and distinct methods, Fourier Transform Infrared Spectroscopy (FTIR) and Ramped Pyrolysis Oxidation (Ramped PyrOx), to examine the quality of organic matter (OM) stored in four peatlands located along a latitudinal gradient (Tropical (4˚N), Subtropical (27˚N), Boreal (48˚N), and Polar (68˚N)). FTIR was used to quantify the relative abundance of carbohydrates, a relatively labile compound class, and aromatics, which are more recalcitrant, in a sample set of four peat cores. These samples were then prepared using Ramped PyrOx, a second, independent method of determining OM quality that mimics the natural diagenetic maturation of OM that would take place over long timescales. Previous large-scale studies using FTIR to evaluate OM quality have observed that it generally increases with increasing latitude (more carbohydrates, less aromatics). Here, we demonstrate that the Ramped PyrOx approach both validates and complements the FTIR approach. The data stemming from each Ramped PyrOx preparation was input to a model that generates an estimated probability density function of the activation energy ( E ) required to break the C bonds in the sample. We separated these functions into three fractions (“low E ,” “medium E ,” and “high E ”) to create Ramped PyrOx variables that could be quantitatively compared to the compound class abundance data from FTIR. In assessing the agreement between the two methods, we found three significant relationships between Ramped PyrOx and FTIR variables. Low E fractions and carbohydrate content were positively correlated (R 2 = 0.51) while low E fractions were negatively correlated with aromatic content (R 2 = 0.58). Medium E fractions were found to be positively correlated with aromatics (R 2 = 0.69).

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood 1 – 7 . The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans 8 – 10 , remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling. The recovery of viral populations from peatland soils across a permafrost thaw gradient provides insights into soil viral diversity, their hosts and the potential impacts on carbon cycling in this environment.

Peatlands historically have acted as a C sink because C-fixation rates exceeded the rate of heterotrophic decomposition. Under future warmer conditions predicted for higher latitudes, however, that balance may shift towards higher rates of heterotrophic respiration leading to the release of previously stored C as CO 2 and CH 4 . The Spruce and Peatlands Response Under Changing Environments (SPRUCE) experiment is designed to test the response of peatlands to climate forcing using a series of warmed enclosures in combination with peat below-ground heating from 0 to +9°C above ambient conditions. This experimental design allowed a test of chemical changes occurring within peatland soils following five years of warming. We analyzed samples in the uppermost 2m of peat using Fourier Transform Infrared Spectroscopy (FT-IR) to quantify the relative abundance of carbohydrate and aromatic compounds in the peat. The peat soils were subjected to deep peat heating (DPH) beginning in June of 2014 followed by whole ecosystem warming (WEW) in August of 2015. We found that the relative amounts of labile and recalcitrant chemical compound groups across the full peat depth interval did not significantly change after five years of exposure to warming. This appears the case even though previous studies have shown that net C losses and loss of bulk peat mass to be instability over that time period. Results suggest that the current store of carbon in peatlands are largely compositionally stable leading to no changes the in the ratio of chemical moieties on the initial four-year timescale of this experiment.

Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH 4 and CO 2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. 3EUUqCyiCvMAAvxFuvvQVm Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations

Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat ( approximately 400 cm and approximately 10 cm from the mat's edge) contrasted with sharply diminished activity at approximately 50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12-20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In contrast, 12-20 cm deep in the sediments microbial communities performing methane-cycling and sulfate reduction persist at lower metabolic rates regardless of mat cover, and may increase activity rapidly when subsurface flow changes.

Warsaw grouper, Hyporthodus nigritus, is a western Atlantic Ocean species typically found at depths between 55 and 525 m. It is listed as a species of concern by the U.S. National Marine Fisheries Service and as near threatened by the International Union for the Conservation of Nature. However, little information exists on the species' life history in the northern Gulf of Mexico (nGOM) and its stock status in that region is currently unknown. Age of nGOM Warsaw grouper was investigated via opaque zone counts in otolith thin sections (max age = 61 y), and then the bomb 14C chronometer was employed to validate the accuracy of age estimates. Otolith cores (n = 14) were analyzed with accelerator mass spectrometry and resulting Δ14C values overlain on a loess regression computed for a regional coral and known-age red snapper Δ14C time series. Residual analysis between predicted Δ14C values from the loess regression versus Warsaw grouper otolith core Δ14C values indicated no significant difference in the two data series. Therefore, the accuracy of otolith-based aging was validated, which enabled growth and longevity estimates to be made for nGOM Warsaw grouper. Dissolved inorganic carbon (DIC) Δ14C values collected from the nGOM support the inference that juvenile Warsaw grouper occur in shelf waters (<200 m) since DIC Δ14C values in this depth range are enriched in 14C and similar to the Δ14C values from otolith cores. A Bayesian model was fit to fishery-dependent age composition data and produced von Bertalanffy growth function parameters of L∞ = 1,533 mm, k = 0.14 y-1, and t0 = 1.82 y. Fishing mortality also was estimated in the model, which resulted in a ratio of fishing to natural mortality of 5.1:1. Overall, study results indicate Warsaw grouper is a long-lived species that is estimated to have experienced significant overfishing in the nGOM, with the age of most landed fish being <10 y.