Response of Methanogens in Arctic Sediments to Temperature and Methanogenic Substrate Availability

Size matters: Aerobic methane oxidation in sediments of shallow thermokarst lakes

Shallow thermokarst lakes are important sources of greenhouse gases (GHGs) such as methane (CH4 ) and carbon dioxide (CO2 ) resulting from continuous permafrost thawing due to global warming. Concentrations of GHGs dissolved in water typically increase with decreasing lake size due to coastal abrasion and organic matter delivery. We hypothesized that (i) CH4 oxidation depends on the natural oxygenation gradient in the lake water and sediments and increases with lake size because of stronger wind-induced water mixing; (ii) CO2 production increases with decreasing lake size, following the dissolved organic matter gradient; and (iii) both processes are more intensive in the upper than deeper sediments due to the in situ gradients of oxygen (O2 ) and bioavailable carbon. We estimated aerobic CH4 oxidation potentials and CO2 production based on the injection of 13 C-labeled CH4 in the 0-10 cm and 10-20 cm sediment depths of small (~300 m2 ), medium (~3000 m2 ), and large (~106  m2 ) shallow thermokarst lakes in the West Siberian Lowland. The CO2 production was 1.4-3.5 times stronger in the upper sediments than in the 10-20 cm depth and increased from large (158 ± 18 nmol CO2  g-1 sediment d.w. h-1 ) to medium and small (192 ± 17 nmol CO2  g-1  h-1 ) lakes. Methane oxidation in the upper sediments was similar in all lakes, while at depth, large lakes had 14- and 74-fold faster oxidation rates (5.1 ± 0.5 nmol CH4 -derived CO2  g-1  h-1 ) than small and medium lakes, respectively. This was attributed to the higher O2 concentration in large lakes due to the more intense wind-induced water turbulence and mixing than in smaller lakes. From a global perspective, the CH4 oxidation potential confirms the key role of thermokarst lakes as an important hotspot for GHG emissions, which increase with the decreasing lake size.

Complexity of temperature dependence in methanogenic microbial environments

There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH₄, an important greenhouse gas. Microbial CH₄ production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO₂ and CH₄. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH₄ production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H₂/CO₂ as immediate CH₄ precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH₄ production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (E_a). Interestingly, CH₄ release from defined microbial cultures, from environmental samples and from wetland field sites all show similar E_a values around 100 kJ mol^-1 indicating that CH₄ production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.

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 freeze-thaw cycles on methanogenic hydrocarbon degradation: Experiment and modeling

Cold regions are warming much faster than the global average, resulting in more frequent and intense freeze-thaw cycles (FTCs) in soils. In hydrocarbon-contaminated soils, FTCs modify the biogeochemical and physical processes controlling petroleum hydrocarbon (PHC) biodegradation and the associated generation of methane (CH₄) and carbon dioxide (CO₂). Thus, understanding the effects of FTCs on the biodegradation of PHCs is critical for environmental risk assessment and the design of remediation strategies for contaminated soils in cold regions. In this study, we developed a diffusion-reaction model that accounts for the effects of FTCs on toluene biodegradation, including methanogenic biodegradation. The model is verified against data generated in a 215 day-long batch experiment with soil collected from a PHC contaminated site in Ontario, Canada. The fully saturated soil incubations with six different treatments were exposed to successive 4-week FTCs, with temperatures oscillating between -10 °C and +15 °C, under anoxic conditions to stimulate methanogenic biodegradation. We measured the headspace concentrations and ¹³C isotope compositions of CH₄ and CO₂ and analyzed the porewater for pH, acetate, dissolved organic and inorganic carbon, and toluene. The numerical model represents solute diffusion, volatilization, sorption, as well as a reaction network of 13 biogeochemical processes. The model successfully simulates the soil porewater and headspace concentration time series data by representing the temperature dependencies of microbial reaction and gas diffusion rates during FTCs. According to the model results, the observed increases in the headspace concentrations of CH₄ and CO₂ by 87% and 136%, respectively, following toluene addition are explained by toluene fermentation and subsequent methanogenesis reactions. The experiment and the numerical simulation show that methanogenic degradation is the primary toluene attenuation mechanism under the electron acceptor-limited conditions experienced by the soil samples, representing 74% of the attenuation, with sorption contributing to 11%, and evaporation contributing to 15%. Also, the model-predicted contribution of acetate-based methanogenesis to total produced CH₄ agrees with that derived from the ¹³C isotope data. The freezing-induced soil matrix organic carbon release is considered as an important process causing DOC increase following each freezing period according to the calculations of carbon balance and SUVA index. The simulation results of a no FTC scenario indicate that, in the absence of FTCs, CO₂ and CH₄ generation would decrease by 29% and 26%, respectively, and that toluene would be biodegraded 23% faster than in the FTC scenario. Because our modeling approach represents the dominant processes controlling PHC biodegradation and the associated CH₄ and CO₂ fluxes, it can be used to analyze the sensitivity of these processes to FTC frequency and duration driven by temperature fluctuations.

Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils

Peatlands are among the largest natural sources of atmospheric methane (CH₄ ) worldwide. Microbial processes play a key role in regulating CH₄ emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH₄ emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi-omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome-metabolome interactions; then explore the competition between methanogens and sulfate-reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO₂ production with temperature. In contrast, the decrease in CH₄ production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait-based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non-limiting sulfate concentrations at 21°C, thereby reducing CH₄ emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low-molecular-weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH₄ emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.

Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies

The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms' shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundances of (i) cofactor, (ii) carrier, and (iii) vitamin biosynthesis, associated with survival metabolism. Additionally, there was the presence of secondary metabolic pathways and defense mechanisms in extreme conditions. Competitive or inhibitory relationships and metabolic patterns were influenced by the physicochemical characteristics of the environments (mainly sulfate concentration) and by human interference (application of biocides and nutrients). Our worldwide baseline study of microbial communities associated with environments of the oil and gas industry will greatly facilitate the establishment of standardized approaches to control MIC.

Hydrobiogechemical interactions in the hyporheic zone of a sulfate-impacted, freshwater stream and riparian wetland ecosystem

Coupled abiotic and biotic processes in the hyporheic zone, where surface water and groundwater mix, play a critical role in the biogeochemical cycling of carbon, nutrients, and trace elements in streams and wetlands. Dynamic hydrologic conditions and anthropogenic pollution can impact redox gradients and biogeochemical response, although few studies examine the resulting hydrobiogeochemical interactions generated within the hyporheic zone. This study examines the effect of hyporheic flux dynamics and anthropogenic sulfate loading on the biogeochemistry of a riparian wetland and stream system. The hydrologic gradient as well as sediment, surface water, and porewater geochemistry chemistry was characterized at multiple points throughout the 2017 spring-summer-fall season at a sulfate-impacted stream flanked by wetlands in northern Minnesota. Results show that organic-rich sediments largely buffer the geochemical responses to brief or low magnitude changes in hydrologic gradient, but sustained or higher magnitude fluxes may variably alter the redox regime and, ultimately, the environmental geochemistry. This has implications for a changing climate that is expected to dramatically alter the hydrological cycle. Further, increased sulfate loading and dissolved or adsorbed ferric iron complexes in the hyporheic zone may induce a cryptic sulfur cycle linked to iron and carbon cycling, as indicated by the abundance of intermediate valence sulfur compounds (e.g., polysulfide, elemental sulfur, thiosulfate) throughout the anoxic wetland and stream-channel sediment column. The observed deviation from a classical redox tower coupled with potential changes in hydraulic gradient in these organic-rich wetland and stream hyporheic zones has implications for nutrient, trace element, and greenhouse gas fluxes into surface water and groundwater, ultimately influencing water quality and global climate.

Global increase in methane production under future warming of lake bottom waters

Lakes are significant emitters of methane to the atmosphere, and thus are important components of the global methane budget. Methane is typically produced in lake sediments, with the rate of methane production being strongly temperature dependent. Local and regional studies highlight the risk of increasing methane production under future climate change, but a global estimate is not currently available. Here, we project changes in global lake bottom temperatures and sediment methane production rates from 1901 to 2099. By the end of the 21st century, lake bottom temperatures are projected to increase globally, by an average of 0.86-2.60°C under Representative Concentration Pathways (RCPs) 2.6-8.5, with greater warming projected at lower latitudes. This future warming of bottom waters will likely result in an increase in methane production rates of 13%-40% by the end of the century, with many low-latitude lakes experiencing an increase of up to 17 times the historical (1970-1999) global average under RCP 8.5. The projected increase in methane production will likely lead to higher emissions from lakes, although the exact magnitude of the emission increase requires more detailed regional studies.

Methanogenesis pathways of methanogens and their responses to substrates and temperature in sediments from the South Yellow Sea

Although coastal sediments are major contributors to the production of atmospheric methane, the effects of environmental conditions on methanogenesis and the community of methanogenic archaea are not well understood. Here, we investigated the methanogenesis pathways in nearshore and offshore sediments from the South Yellow Sea (SYS). Moreover, the effects of the supply of methanogenic substrates (H₂/CO₂, acetate, trimethylamine (TMA), and methanol) and temperature on methanogenesis and the community of methanogenic archaea were further determined. Methylotrophic, hydrogenotrophic and acetotrophic methanogenesis were found to be responsible for biogenic methane production in nearshore sediments. In the offshore sediments, methylotrophic methanogenesis was the predominant methanogenic pathway. The changes in methanogenic community structure under different substrate amendments were characterized. Lower diversities were detected in substrate-amended samples with methanogenic activity. Hydrogenotrophic Methanogenium, multitrophic Methanosarcina, methylotrophic Methanococcoide, Methanococcoide or methylotrophic Methanolobus were dominant in H₂/CO₂-, acetate-, TMA- and methanol-amended sediment slurries, respectively. PCoA showed that the methanogen community in H₂/CO₂ and acetate amendments exhibited greater differences than those in other treatments. Lower temperature (10 °C) limits hydrogenotrophic and acetoclastic methanogenesis, but methylotrophic methanogenesis is much less affected. The response of methanogen diversity to the incubation temperature varied among the different substrate-amended slurries. The multitrophic methanogen Methanosarcina became increasingly abundant in H₂/CO_2- and acetate-amended sediment slurries when the temperature increased from 10 to 30 °C.

Amsterdam urban canals contain novel niches for methane-cycling microorganisms

Urbanised environments have been identified as hotspots of anthropogenic methane emissions. Especially urban aquatic ecosystems are increasingly recognised as important sources of methane. However, the microbiology behind these emissions remains unexplored. Here, we applied microcosm incubations and molecular analyses to investigate the methane‐cycling community of the Amsterdam canal system in the Netherlands. The sediment methanogenic communities were dominated by Methanoregulaceae and Methanosaetaceae, with co‐occurring methanotrophic Methanoperedenaceae and Methylomirabilaceae indicating the potential for anaerobic methane oxidation. Methane was readily produced after substrate amendment, suggesting an active but substrate‐limited methanogenic community. Bacterial 16S rRNA gene amplicon sequencing of the sediment revealed a high relative abundance of Thermodesulfovibrionia. Canal wall biofilms showed the highest initial methanotrophic potential under oxic conditions compared to the sediment. During prolonged incubations the maximum methanotrophic rate increased to 8.08 mmol g_DW⁻¹ d⁻¹ that was concomitant with an enrichment of Methylomonadaceae bacteria. Metagenomic analysis of the canal wall biofilm lead to the recovery of a single methanotroph metagenome‐assembled genome. Taxonomic analysis showed that this methanotroph belongs to the genus Methyloglobulus. Our results underline the importance of previously unidentified and specialised environmental niches at the nexus of the natural and human‐impacted carbon cycle.

Temperature differently affected methanogenic pathways and microbial communities in sub-Antarctic freshwater ecosystems

Freshwater ecosystems are responsible for an important part of the methane (CH₄) emissions which are likely to change with global warming. This study aims to evaluate temperature-induced (from 5 to 20 °C) changes on microbial community structure and methanogenic pathways in five sub-Antarctic lake sediments from Magallanes strait to Cape Horn, Chile. We combined in situ CH₄ flux measurements, CH₄ production rates (MPRs), gene abundance quantification and microbial community structure analysis (metabarcoding of the 16S rRNA gene). Under unamended conditions, a temperature increase of 5 °C doubled MPR while microbial community structure was not affected. Stimulation of methanogenesis by methanogenic precursors as acetate and H₂/CO₂, resulted in an increase of MPRs up to 127-fold and 19-fold, respectively, as well as an enrichment of mcrA-carriers strikingly stronger under acetate amendment. At low temperatures, H₂/CO₂-derived MPRs were considerably lower (down to 160-fold lower) than the acetate-derived MPRs, but the contribution of hydrogenotrophic methanogenesis increased with temperature. Temperature dependence of MPRs was significantly higher in incubations spiked with H₂/CO₂ (c. 1.9 eV) compared to incubations spiked with acetate or unamended (c. 0.8 eV). Temperature was not found to shape the total microbial community structure, that rather exhibited a site-specific variability among the studied lakes. However, the methanogenic archaeal community structure was driven by amended methanogenic precursors with a dominance of Methanobacterium in H₂/CO₂-based incubations and Methanosarcina in acetate-based incubations. We also suggested the importance of acetogenic H₂-production outcompeting hydrogenotrohic methanogenesis especially at low temperatures, further supported by homoacetogen proportion in the microcosm communities. The combination of in situ-, and laboratory-based measurements and molecular approaches indicates that the hydrogenotrophic pathway may become more important with increasing temperatures than the acetoclastic pathway. In a continuously warming environment driven by climate change, such issues are crucial and may receive more attention.

Impact of river channel lateral migration on microbial communities across a discontinuous permafrost floodplain

Permafrost soils store approximately twice the amount of carbon currently present in Earth's atmosphere and are acutely impacted by climate change due to the polar amplification of increasing global temperature. Many organic-rich permafrost sediments are located on large river floodplains, where river channel migration periodically erodes and re-deposits the upper tens of meters of sediment. Channel migration exerts a first-order control on the geographic distribution of permafrost and floodplain stratigraphy and thus may affect microbial habitats. To examine how river channel migration in discontinuous permafrost environments affects microbial community composition, we used amplicon sequencing of the 16S rRNA gene on sediment samples from floodplain cores and exposed riverbanks along the Koyukuk River, a large tributary of the Yukon River in west-central Alaska. Microbial communities are sensitive to permafrost thaw: communities found in deep samples thawed by the river closely resembled near-surface active layer communities in non-metric multidimensional scaling analyses but did not resemble floodplain permafrost communities at the same depth. Microbial communities also displayed lower diversity and evenness in permafrost than in both the active layer and permafrost-free point bars recently deposited by river channel migration. Taxonomic assignments based on 16S and quantitative PCR for the methyl-coenzyme M reductase functional gene demonstrated that methanogens and methanotrophs are abundant in older permafrost-bearing deposits, but not in younger, non-permafrost point bar deposits. The results suggested that river migration, which regulates the distribution of permafrost, also modulates the distribution of microbes potentially capable of producing and consuming methane on the Koyukuk River floodplain. Importance Arctic lowlands contain large quantities of soil organic carbon that is currently sequestered in permafrost. With rising temperatures, permafrost thaw may allow this carbon to be consumed by microbial communities and released to the atmosphere as carbon dioxide or methane. We used gene sequencing to determine the microbial communities present in the floodplain of a river running through discontinuous permafrost. We found the river's lateral movement across its floodplain influences the occurrence of certain microbial communities-in particular, methane-cycling microbes were present on the older, permafrost-bearing eroding riverbank but absent on the newly deposited river bars. Riverbank sediment had microbial communities more similar to the floodplain active layer than permafrost samples from the same depth. Therefore, spatial patterns of river migration influence the distribution of microbial taxa relevant to the warming Arctic climate.

Greenhouse gas production and lipid biomarker distribution in Yedoma and Alas thermokarst lake sediments in Eastern Siberia

Permafrost thaw leads to thermokarst lake formation and talik growth tens of meters deep, enabling microbial decomposition of formerly frozen organic matter (OM). We analyzed two 17-m-long thermokarst lake sediment cores taken in Central Yakutia, Russia. One core was from an Alas lake in a Holocene thermokarst basin that underwent multiple lake generations, and the second core from a young Yedoma upland lake (formed ~70 years ago) whose sediments have thawed for the first time since deposition. This comparison provides a glance into OM fate in thawing Yedoma deposits. We analyzed total organic carbon (TOC) and dissolved organic carbon (DOC) content, n-alkane concentrations, and bacterial and archaeal membrane markers. Furthermore, we conducted 1-year-long incubations (4°C, dark) and measured anaerobic carbon dioxide (CO₂ ) and methane (CH₄ ) production. The sediments from both cores contained little TOC (0.7 ± 0.4 wt%), but DOC values were relatively high, with the highest values in the frozen Yedoma lake sediments (1620 mg L^-1 ). Cumulative greenhouse gas (GHG) production after 1 year was highest in the Yedoma lake sediments (226 ± 212 µg CO₂ -C g^-1  dw, 28 ± 36 µg CH₄ -C g^-1  dw) and 3 and 1.5 times lower in the Alas lake sediments, respectively (75 ± 76 µg CO₂ -C g^-1  dw, 19 ± 29 µg CH₄ -C g^-1  dw). The highest CO₂ production in the frozen Yedoma lake sediments likely results from decomposition of readily bioavailable OM, while highest CH₄ production in the non-frozen top sediments of this core suggests that methanogenic communities established upon thaw. The lower GHG production in the non-frozen Alas lake sediments resulted from advanced OM decomposition during Holocene talik development. Furthermore, we found that drivers of CO₂ and CH₄ production differ following thaw. Our results suggest that GHG production from TOC-poor mineral deposits, which are widespread throughout the Arctic, can be substantial. Therefore, our novel data are relevant for vast ice-rich permafrost deposits vulnerable to thermokarst formation.

Gas ebullition from petroleum hydrocarbons in aquatic sediments: A review

Gas ebullition in sediment results from biogenic gas production by mixtures of bacteria and archaea. It often occurs in organic-rich sediments that have been impacted by petroleum hydrocarbon (PHC) and other anthropogenic pollution. Ebullition occurs under a relatively narrow set of biological, chemical, and sediment geomechanical conditions. This process occurs in three phases: I) biogenic production of primarily methane and dissolved phase transport of the gases in the pore water to a bubble nucleation site, II) bubble growth and sediment fracture, and III) bubble rise to the surface. The rate of biogenic gas production in phase I and the resistance of the sediment to gas fracture in phase II play the most significant roles in ebullition kinetics. What is less understood is the role that substrate structure plays in the rate of methanogenesis that drives gas ebullition. It is well established that methanogens have a very restricted set of compounds that can serve as substrates, so any complex organic molecule must first be broken down to fermentable compounds. Given that most ebullition-active sediments are completely anaerobic, the well-known difficulty in degrading PHCs under anaerobic conditions suggests potential limitations on PHC-derived gas ebullition. To date, there are no studies that conclusively demonstrate that weathered PHCs can alone drive gas ebullition. This review consists of an overview of the factors affecting gas ebullition and the biochemistry of anaerobic PHC biodegradation and methanogenesis in sediment systems. We next compile results from the scholarly literature on PHCs serving as a source of methanogenesis. We combine these results to assess the potential for PHC-driven gas ebullition using energetics, kinetics, and sediment geomechanics analyses. The results suggest that short chain <C₁₀ alkanes are the only PHC class that alone may have the potential to drive ebullition, and that PHC-derived methanogenesis likely plays a minor part in driving gas ebullition in contaminated sediments compared to natural organic matter.

An Unexpectedly Broad Thermal and Salinity-Tolerant Estuarine Methanogen Community

Moderately thermophilic (T_max, ~55 °C) methanogens are identified after extended enrichments from temperate, tropical and low-temperature environments. However, thermophilic methanogens with higher growth temperatures (T_opt ≥ 60 °C) are only reported from high-temperature environments. A microcosm-based approach was used to measure the rate of methane production and methanogen community structure over a range of temperatures and salinities in sediment from a temperate estuary. We report short-term incubations (<48 h) revealing methanogens with optimal activity reaching 70 °C in a temperate estuary sediment (in situ temperature 4–5 °C). While 30 °C enrichments amended with acetate, H₂ or methanol selected for corresponding mesophilic trophic groups, at 60 °C, only hydrogenotrophs (genus Methanothermobacter) were observed. Since these methanogens are not known to be active under in situ temperatures, we conclude constant dispersal from high temperature habitats. The likely provenance of the thermophilic methanogens was studied by enrichments covering a range of temperatures and salinities. These enrichments indicated that the estuarine sediment hosted methanogens encompassing the global activity envelope of most cultured species. We suggest that estuaries are fascinating sink and source environments for microbial function study.

Long-term enriched methanogenic communities from thermokarst lake sediments show species-specific responses to warming

Thermokarst lakes are large potential greenhouse gas (GHG) sources in a changing Arctic. In a warming world, an increase in both organic matter availability and temperature is expected to boost methanogenesis and potentially alter the microbial community that controls GHG fluxes. These community shifts are, however, challenging to detect by resolution-limited 16S rRNA gene-based approaches. Here, we applied full metagenome sequencing on long-term thermokarst lake sediment enrichments on acetate and trimethylamine at 4°C and 10°C to unravel species-specific responses to the most likely Arctic climate change scenario. Substrate amendment was used to mimic the increased organic carbon availability upon permafrost thaw. By performing de novo assembly, we reconstructed five high-quality and five medium-quality metagenome-assembled genomes (MAGs) that represented 59% of the aligned metagenome reads. Seven bacterial MAGs belonged to anaerobic fermentative bacteria. Within the Archaea, the enrichment of methanogenic Methanosaetaceae/Methanotrichaceae under acetate amendment and Methanosarcinaceae under trimethylamine (TMA) amendment was not unexpected. Surprisingly, we observed temperature-specific methanogenic (sub)species responses with TMA amendment. These highlighted distinct and potentially functional climate-induced shifts could not be revealed with 16S rRNA gene-based analyses. Unraveling these temperature- and nutrient-controlled species-level responses is essential to better comprehend the mechanisms that underlie GHG production from Arctic lakes in a warming world.

Semi-continuous feeding combined with traditional domestication improved anaerobic performance during treatment of cassava stillage

The effects of feeding pattern were studied during anaerobic digestion of cassava stillage. Continuous feeding and semi-continuous feeding, were adopted in two internal circulation (IC) reactors (A and B, respectively). The reactors showed different performance in the anaerobic digestion process. The maximum difference, was observed for the soluble chemical oxygen demand (SCOD) removal rate and the biogas production, which were 23.2% and 95.7 L/2 d higher in reactor B than reactor A, respectively. The overall VFAs level of reactor A was higher than that of reactor B. Microbial community analyses indicated that the abundances of dominant bacteria and methanogens became higher in the reactor B than in reactor A as the digestion process progressed. Hence, semi-continuous feeding showed superior performance than continuous feeding for SCOD removal rate, biogas production, and the relative abundances of methanogens in the case of high OLR.

Impact of Warming on Greenhouse Gas Production and Microbial Diversity in Anoxic Peat From a Sphagnum-Dominated Bog (Grand Rapids, Minnesota, United States)

Climate warming is predicted to increase heterotrophic metabolism in northern peatland soils leading to enhanced greenhouse gas emissions. However, the specific relationships between temperature and the greenhouse gas producing microbial communities are poorly understood. Thus, in this study, the temperature dependence of carbon dioxide (CO2) and methane (CH4) production rates along with abundance and composition of microbial communities were investigated in peat from a Sphagnum-dominated peatland, S1 bog (Minnesota, United States). Whereas CH4 production rates increased with temperature up to 30°C, CO2 production did not, resulting in a lower CO2:CH4 ratio with increasing temperature. CO2 production showed both psychrophilic and mesophilic maxima at 4 and 20°C, respectively, and appears to be mediated by two anaerobic microbial communities, one that operates under psychrophilic conditions that predominate for much of the year, and another that is more active under warmer conditions during the growing season. In incubations at 10°C above the ambient range, members of the Clostridiaceae and hydrogenotrophic methanogens of the Methanobacteriaceae dominated. Moreover, a significant negative correlation between temperature and microbial diversity was observed. Results indicate that the potential consequences of warming surface peat in northern peatlands include a large stimulation in CH4 production and a significant loss of microbial diversity.

Dynamics of microbial communities and CO2 and CH4 fluxes in the tundra ecosystems of the changing Arctic

Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO₂ and CH₄) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO₂ and CH₄ emissions.

Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations

Microorganisms can use crystalline iron minerals for iron reduction linked to organic matter degradation or as conduits for direct interspecies electron transfer (mDIET) to syntrophic partners, e.g., methanogens. The environmental conditions that lead either to reduction or conduit use are so far unknown. We investigated microbial community shifts and interactions with crystalline iron minerals (hematite and magnetite) in methanic ferruginous marine sediment incubations during organic matter (glucose) degradation at varying temperatures. Iron reduction rates increased with decreasing temperature from 30°C to 4°C. Both hematite and magnetite facilitated iron reduction at 4°C, demonstrating that microorganisms in the methanic zone of marine sediments can reduce crystalline iron oxides under psychrophilic conditions. Methanogenesis occurred, however, at higher rates with increasing temperature. At 30°C, both hematite and magnetite accelerated methanogenesis onset and maximum process rates. At lower temperatures (10°C and 4°C), hematite could still facilitate methanogenesis but magnetite served more as an electron acceptor for iron reduction than as a conduit. Different temperatures selected for different key microorganisms: at 30°C, members of genus Orenia, Halobacteroidaceae, at 10°C, Photobacterium and the order Clostridiales, and at 4°C Photobacterium and Psychromonas were enriched. Members of the order Desulfuromonadales harboring known dissimilatory iron reducers were also enriched at all temperatures. Our results show that crystalline iron oxides predominant in some natural environments can facilitate electron transfer between microbial communities at psychrophilic temperatures. Furthermore, temperature has a critical role in determining the pathway of crystalline iron oxide utilization in marine sediment shifting from conduction at 30°C to predominantly iron reduction at lower temperatures.

Eutrophication exacerbates the impact of climate warming on lake methane emission

Net methane (CH₄) emission from lakes depends on two antagonistic processes: CH₄ production (methanogenesis) and CH₄ oxidation (methanotrophy). It is unclear how climate warming will affect the balance between these processes, particularly among lakes of different trophic status. Here we show that methanogenesis is more sensitive to temperature than methanotrophy, and that eutrophication magnifies this temperature sensitivity. Using laboratory incubations of water and sediment from ten tropical, temperate and subarctic lakes with contrasting trophic states, ranging from oligotrophic to hypereutrophic, we explored the temperature sensitivity of methanogenesis and methanotrophy. We found that both processes presented a higher temperature sensitivity in tropical lakes, followed by temperate, and subarctic lakes; but more importantly, we found that eutrophication triggered a higher temperature sensitivity. A model fed by our empirical data revealed that increasing lake water temperature by 2 °C leads to a net increase in CH₄ emissions by 101-183% in hypereutrophic lakes and 47-56% in oligotrophic lakes. We conclude that climate warming will tilt the CH₄ balance towards higher lake emission and that this impact will be exacerbated by the eutrophication of the lakes.

Increases in temperature and nutrient availability positively affect methane-cycling microorganisms in Arctic thermokarst lake sediments

Arctic permafrost soils store large amounts of organic matter that is sensitive to temperature increases and subsequent microbial degradation to methane (CH₄) and carbon dioxide (CO₂). Here, we studied methanogenic and methanotrophic activity and community composition in thermokarst lake sediments from Utqiag˙vik (formerly Barrow), Alaska. This experiment was carried out under in situ temperature conditions (4°C) and the IPCC 2013 Arctic climate change scenario (10°C) after addition of methanogenic and methanotrophic substrates for nearly a year. Trimethylamine (TMA) amendment with warming showed highest maximum CH₄production rates, being 30% higher at 10°C than at 4°C. Maximum methanotrophic rates increased by up to 57% at 10°C compared to 4°C. 16S rRNA gene sequencing indicated high relative abundance of Methanosarcinaceae in TMA amended incubations, and for methanotrophic incubations Methylococcaeae were highly enriched. Anaerobic methanotrophic activity with nitrite or nitrate as electron acceptor was not detected. This study indicates that the methane cycling microbial community can adapt to temperature increases and that their activity is highly dependent on substrate availability.

Non-Psychrophilic Methanogens Capable of Growth Following Long-Term Extreme Temperature Changes, with Application to Mars

Although the martian environment is currently cold and dry, geomorphological features on the surface of the planet indicate relatively recent (<4 My) freeze/thaw episodes. Additionally, the recent detections of near-subsurface ice as well as hydrated salts within recurring slope lineae suggest potentially habitable micro-environments within the martian subsurface. On Earth, microbial communities are often active at sub-freezing temperatures within permafrost, especially within the active layer, which experiences large ranges in temperature. With warming global temperatures, the effect of thawing permafrost communities on the release of greenhouse gases such as carbon dioxide and methane becomes increasingly important. Studies examining the community structure and activity of microbial permafrost communities on Earth can also be related to martian permafrost environments, should life have developed on the planet. Here, two non-psychrophilic methanogens, Methanobacterium formicicum and Methanothermobacter wolfeii, were tested for their ability to survive long-term (~4 year) exposure to freeze/thaw cycles varying in both temperature and duration, with implications both for climate change on Earth and possible life on Mars.

Rate of warming affects temperature sensitivity of anaerobic peat decomposition and greenhouse gas production

Temperature sensitivity of anaerobic carbon mineralization in wetlands remains poorly represented in most climate models and is especially unconstrained for warmer subtropical and tropical systems which account for a large proportion of global methane emissions. Several studies of experimental warming have documented thermal acclimation of soil respiration involving adjustments in microbial physiology or carbon use efficiency (CUE), with an initial decline in CUE with warming followed by a partial recovery in CUE at a later stage. The variable CUE implies that the rate of warming may impact microbial acclimation and the rate of carbon-dioxide (CO₂ ) and methane (CH₄ ) production. Here, we assessed the effects of warming rate on the decomposition of subtropical peats, by applying either a large single-step (10°C within a day) or a slow ramping (0.1°C/day for 100 days) temperature increase. The extent of thermal acclimation was tested by monitoring CO₂ and CH₄ production, CUE, and microbial biomass. Total gaseous C loss, CUE, and MBC were greater in the slow (ramp) warming treatment. However, greater values of CH₄ -C:CO₂ -C ratios lead to a greater global warming potential in the fast (step) warming treatment. The effect of gradual warming on decomposition was more pronounced in recalcitrant and nutrient-limited soils. Stable carbon isotopes of CH₄ and CO₂ further indicated the possibility of different carbon processing pathways under the contrasting warming rates. Different responses in fast vs. slow warming treatment combined with different endpoints may indicate alternate pathways with long-term consequences. Incorporations of experimental results into organic matter decomposition models suggest that parameter uncertainties in CUE and CH₄ -C:CO₂ -C ratios have a larger impact on long-term soil organic carbon and global warming potential than uncertainty in model structure, and shows that particular rates of warming are central to understand the response of wetland soils to global climate change.

Methanogen Population of an Oil Production Skimmer Pit and the Effects of Environmental Factors and Substrate Availability on Methanogenesis and Corrosion Rates

Assessment of microbial communities from an oil production skimmer pit using 16S rRNA gene sequencing technique revealed massive dominance of methanogenic archaea in both the skimmer pit water and sediment samples. The dominant genera of methanogens involved are mostly the acetotrophic Methanosaeta (36-83 %), and the hydrogenotrophic Methanococcus (49 %) indicating that methanogenesis is the dominant terminal metabolic process in the skimmer pit. Further studies showed that the methanogens had their optimal activity at pH 6-6.5, salinity of 100 mM, and temperature of 35-45 °C. When appropriate substrates are available and utilized by methanogens, methane production correlates with general corrosion rates (r = +0.927; p < 0.01), and under different conditions of pH, salinity and temperature, methane production showed significantly strong positive correlations (r = +0.824, +0.827, and +0.805; p < 0.01, respectively) with general corrosion rates. To the best of our knowledge, this research work was the first to assess microbial community composition of an oil production skimmer pit at Escravos facility in Nigeria.

Methanogenic Hydrocarbon Degradation: Evidence from Field and Laboratory Studies

Microbial transformation of hydrocarbons to methane is an environmentally relevant process taking place in a wide variety of electron acceptor-depleted habitats, from oil reservoirs and coal deposits to contaminated groundwater and deep sediments. Methanogenic hydrocarbon degradation is considered to be a major process in reservoir degradation and one of the main processes responsible for the formation of heavy oil deposits and oil sands. In the absence of external electron acceptors such as oxygen, nitrate, sulfate or Fe(III), fermentation and methanogenesis become the dominant microbial metabolisms. The major end product under these conditions is methane, and the only electron acceptor necessary to sustain the intermediate steps in this process is CO2, which is itself a net product of the overall reaction. We are summarizing the state of the art and recent advances in methanogenic hydrocarbon degradation research. Both the key microbial groups involved as well as metabolic pathways are described, and we discuss the novel insights into methanogenic hydrocarbon-degrading populations studied in laboratory as well as environmental systems enabled by novel cultivation-based and molecular approaches. Their possible implications on energy resources, bioremediation of contaminated sites, deep-biosphere research, and consequences for atmospheric composition and ultimately climate change are also addressed.

Microbial diversity and functional capacity in polar soils

Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions.

A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity

River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4-30°C, pH 6-8, 1-15 g l(-1) NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus-related species at 4-21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l(-1) selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.