Methanogenesis from methanol at low temperatures by a novel psychrophilic methanogen, "Methanolobus psychrophilus" sp. nov., prevalent in Zoige wetland of the Tibetan plateau

High methane ebullition throughout one year in a regulated central European stream

Ebullition transports large amounts of the potent greenhouse gas methane (CH4 ) from aquatic sediments to the atmosphere. River beds are a main source of biogenic CH4 , but emission estimates and the relative contribution of ebullition as a transport pathway are poorly constrained. This study meets a need for more direct measurements with a whole-year data set on CH4 ebullition from a small stream in southern Germany. Four gas traps were installed in a cross section in a river bend, representing different bed substrates between undercut and slip-off slope. For a comparison, diffusive fluxes were estimated from concentration gradients in the sediment and from measurements of dissolved CH4 in the surface water. The data revealed highest activity with gas fluxes above 1000 ml m- 2  d- 1 in the center of the stream, sustained ebullition during winter, and a larger contribution of ebullitive compared to diffusive CH4 fluxes. Increased gas fluxes from the center of the river may be connected to greater exchange with the surface water, thus increased carbon and nutrient supply, and a higher sediment permeability for gas bubbles. By using stable isotope fractionation, we estimated that 12-44% of the CH4 transported diffusively was oxidized. Predictors like temperature, air pressure drop, discharge, or precipitation could not or only poorly explain temporal variations of ebullitive CH4 fluxes.

Stochastic processes drive the diversity and composition of methanogenic community in a natural mangrove ecosystem

Methanogens are considered to be crucial components of mangrove ecosystems with ecological significance. However, understanding the assembly processes of methanogenic communities in mangrove ecosystems is relatively insufficient. In the current study, a natural mangrove in a protection zone was employed to investigate the diversity and assembly processes of methanogenic community by using amplicon high-throughput sequencing, a null model as well as a neutral community model. The results showed that methanogenic community in mangrove sediments were highly diverse, with the predominance of methylotrophic Methanolobus, and hydrogenotrophic Methanogenium, Methanospirillum. The diversity, composition, and gene abundance varied obviously across the mangrove sampling sites, whereas the measured environmental variables exhibited a negligible effect. Null model showed that the values of beta nearest-taxon index were mostly between -2 and 2, indicating that stochastic processes contributed more than deterministic processes driving the methanogenic community assembly in mangrove sediments. Neutral community model revealed a high estimated migration rate of methanogenic community, further substantiating the significance of stochastic processes. Among the keystone species identified in network analysis, methanogens affiliated to hydrogenotrophic Methanospirillum may have a crucial role in maintaining the structure and function of methanogenic community. Notably, these keystone species were almost unaffected by measured environmental factors, indicating that the methanogenic community in mangrove sediments is more likely to be affected by stochastic processes. This study deepens the understanding of the diversity and assembly of methanogenic community in mangrove sediments, and provides clues to maintain mangrove ecosystem functioning.

Methanolobus mangrovi sp. nov. and Methanolobus sediminis sp. nov, two novel methylotrophic methanogens isolated from mangrove sediments in China

Two methylotrophic methanogens, designated strains FTZ2T and FTZ6T, were isolated from mangrove sediment sampled in Futian Mangrove Nature Reserve in Shenzhen, PR China. Cells of strains FTZ2T and FTZ6T were cocci, with diameters of 0.6-1.0 µm and 0.6-0.9 µm, respectively. Both strains grew on methanol, methylamine, dimethylamine and trimethylamine, but not on acetate, formate, H2/CO2, choline, betaine or dimethyl sulphide. Strain FTZ2T grew at 10-37 °C (optimally at 33 °C), pH 5.5-8.0 (optimally at pH 7.0) and 0-1.03 M NaCl (optimally at 0.17 M NaCl). In contrast, strain FTZ6T grew at 15-42 °C (optimally at 37 °C), pH 5.0-7.5 (optimally pH 6.5) and 0-1.03 M NaCl (optimally at 0.17 M NaCl). Both strains required magnesium for growth and were susceptible to sodium dodecyl sulphate. Biotin was required for the growth of strain FTZ2T but not of strain FTZ6T. The genomic G+C contents of strains FTZ2T and FTZ6T were 41.6 and 40.9 mol%, respectively. Phylogenetic analyses revealed that strain FTZ2T was mostly related to Methanolobus psychrotolerans YSF-03T, with 16S rRNA gene similarity of 98.6 %, an average nucleotide identity (ANI) of 82.5 %, and a digital DNA-DNA hybridization (dDDH) of 24.6 %. While strain FTZ6T was mostly related to Methanolobus vulcani PL-12/MT, with 16S rRNA gene similarity of 99.4 %, an ANI of 88.6% and a dDDH of 34.6 %. Based on phenotypic, phylogenetic and genotypic evidence, two novel species of the genus Methanolobus, Methanolobus mangrovi sp. nov. and Methanolobus sediminis sp. nov., are proposed. The type strain of M. mangrovi sp. nov. is FTZ2T (=CCAM 1276T=JCM 39396T) and the type strain of M. sediminis sp. nov. is FTZ6T (=CCAM 1277T=JCM 39397T).

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.

Methyl-Based Methanogenesis: an Ecological and Genomic Review

Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.

Research trends and strategies for the improvement of anaerobic digestion of food waste in psychrophilic temperatures conditions

The organic fraction of municipal solid waste is mainly composed of food waste (FW), and traditional disposal practices for this fraction are generally considered to have negative environmental and economic impacts. However, the organic characteristics of this fraction could also be exploited through the anaerobic digestion of FW (FW-AD), which represents unique advantages, including the reduction of the area required for final disposal and environmental pollution and the same time the generation of renewable energy (mainly methane gas), and a by-product for agricultural use (digestate) due to its high nutrient content. Although approximately 88% of the world's population resides in areas with temperatures below 8 °C, psychrophilic conditions (temperatures below 20 °C) have hardly been studied, while mesophilic (66%) and thermophilic (27%) ranges were found to be more common than psychrophilic FW-AD (7%). The latter condition could decrease microbial activity and organic matter removal, which could affect biogas production and even make AD unfeasible. To improve the efficiency of the psychrophilic FW-AD process, there are strategies such as: measurement of physical properties as particle size, rheological characteristics (viscosity, consistency index and substrate behavior index), density and humidity, bioaugmentation and co-digestion with other substrates, use of inocula with psychrophilic methanogenic communities, reactor heating and modification of reactor configurations. However, these variables have hardly been studied in the context of psychrophilic conditions and future research should focus on evaluating the influence of these variables on FW-AD under psychrophilic conditions. Through a bibliometric analysis, this paper has described and analyzed the FW-AD process, with a focus on the psychrophilic conditions (<20 °C) so as to identify advances and future research trends, as well as determine strategies toward improving the anaerobic process under low temperature conditions.

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Temperature has a great influence on anaerobic digestion of food waste (FW-AD).

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Studies on the psychrophilic condition are limited, warranting further research.

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Physical properties of the substrate and inoculum influence psychrophilic FW-AD.

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The use of inocula adapted to low temperatures could increase biogas production.

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Changes in reactor configurations could improve biogas yield at low temperature.

The synergy of Fe(III) and NO2- drives the anaerobic oxidation of methane

The anaerobic oxidation of methane (AOM) driven by NO₂^- or Fe(III) alone was limited by slow electron delivery and ineffective enrichment of microbes. The flexible coupling between Fe(III) and NO₂^- potentially cooperated to accelerate AOM. One negative control was fed CH₄ and NO₂^-, and four treatment reactors were supplemented with CH₄, NO₂^- and ferric citrate (FC)/ferric chloride (FCH)/ chelate iron (FCI)/ferric hydroxide (FH) and were anaerobically operated for 1200 days to verify the synergy and promicrobial roles of Fe(III) and NO₂^- in improving AOM. The changes in gas and ion profiles were observed in the reactors, and microbial development was studied using 16S rRNA gene sequencing with the Illumina platform. The results indicated that the combined Fe(III) and NO₂^- treatment improved AOM, and their synergy followed the order of FC > FCI > FCH > FH. The biochemical reaction of Fe³⁺ with NO₂^- and its secondary process accelerated electron transfer to microbial cells and subsequently enhanced AOM in the reactors. The total organic carbon (TOC) content, NH₄⁺ content, NO₃^- content, and pH value altered the dominant bacteria the most in the FC reactor, FCI, FCH, and FH groups, respectively. Several dominant bacterial species were enriched, whereas only two archaea were highly concentrated in the FC and FCI groups. Only bacteria were detected in the FCH group, and archaea contributed substantially to the FH group. These findings contribute to an improved understanding of the interactions among nitrogen, iron and CH₄ that are paramount to accelerating the process of AOM for engineering applications.

Microbial drivers of methane emissions from unrestored industrial salt ponds

Wetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

Anaerobic methane oxidation linked to Fe(III) reduction in a Candidatus Methanoperedens-enriched consortium from the cold Zoige wetland at Tibetan Plateau

Anaerobic oxidation of methane (AOM) is a microbial process degrading ample methane in anoxic environments, and Ca. Methanoperedens mediated nitrate- or metal-reduction linked AOM is believed important in freshwater systems. This work, via 16S rRNA gene diversity survey and 16S rRNA quantification, found abundant Ca. Methanoperedens along with iron in the cold Zoige wetland at Tibetan Plateau. The wetland soil microcosm performed Fe(III) reduction, rather than nitrate- nor sulphate-reduction, coupled methane oxidation (3.87 μmol d^-1 ) with 32.33 μmol Fe(II) accumulation per day at 18°C, but not at 30°C. A metagenome-assembled genome (MAG) recovered from the microcosm exhibits ~74% average nucleotide identity with the reported Ca. Methanoperedens spp. that perform Fe(III) reduction linked AOM, thus a novel species Ca. Methanoperedens psychrophilus was proposed. Ca. M. psychrophilus contains the whole suite of CO₂ reductive methanogenic genes presumably involving in AOM via a reverse direction, and comparative genome analysis revealed its unique gene categories: the multi-heme clusters (MHCs) cytochromes, the S-layer proteins highly homologous to those recovered from lower temperature environments and type IV pili, those could confer Ca. M. psychrophilus of cold adaptability. Therefore, this work reports the first methanotroph implementing AOM in an alpine wetland.

Seasonal Dynamics of Bathyarchaeota-Dominated Benthic Archaeal Communities Associated with Seagrass (Zostera japonica) Meadows

Little is known about the seasonal dynamic of archaeal communities and their potential ecological functions in temperate seagrass ecosystems. In this study, seasonal changes in diversity, community structure, and potential metabolic functions of benthic archaea in surface sediments of two seagrass meadows along the northern Bohai Sea in China were investigated using Miseq sequencing of the 16S rRNA gene and Tax4Fun2 functional prediction. Overall, Crenarchaeota (mainly Bathy-15, Bathy-8, and Bathy-6) dominated, followed by Thermoplasmatota, Asgardarchaeota, and Halobacterota, in terms of alpha diversities and relative abundance. Significant seasonal changes in the entire archaeal community structure were observed. The major phyla Methanobacteria, Nitrosopumilales, and genus Methanolobus had higher proportions in spring, while MBG-D and Bathyarchaeota were more abundant in summer and autumn, respectively. Alpha diversities (Shannon and Simpson) were the highest in summer and the lowest in autumn (ANOVA test, p < 0.05). Salinity, total organic carbon, and total organic nitrogen were the most significant factors influencing the entire archaeal community. Higher cellulose and hemicellulose degradation potentials occurred in summer, while methane metabolism potentials were higher in winter. This study indicated that season had strong effects in modulating benthic archaeal diversity and functional potentials in the temperate seagrass ecosystems.

Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern

Anaerobic archaeal methanogens are key players in the global carbon cycle due to their role in the final stages of organic matter decomposition in anaerobic environments such as wetland sediments. Here we present the first draft metagenome-assembled genome (MAG) sequence of an unclassified Methanosarcinaceae methanogen phylogenetically placed adjacent to the Methanolobus and Methanomethylovorans genera that appears to be a distinct genus and species. The genome is derived from sediments of a hypersaline (97–148 ppt chloride) unrestored industrial saltern that has been observed to be a significant methane source. The source sediment is more saline than previous sources of Methanolobus and Methanomethylovorans. We propose a new genus name, Methanosalis, to house this genome, which we designate with the strain name SBSPR1A. The MAG was binned with CONCOCT and then improved via scaffold extension and reassembly. The genome contains pathways for methylotrophic methanogenesis from trimethylamine and dimethylamine, as well as genes for the synthesis and transport of compatible solutes. Some genes involved in acetoclastic and hydrogenotrophic methanogenesis are present, but those pathways appear incomplete in the genome. The MAG was more abundant in two former industrial salterns than in a nearby reference wetland and a restored wetland, both of which have much lower salinity levels, as well as significantly lower methane emissions than the salterns.

Bacteria and archaea involved in anaerobic mercury methylation and methane oxidation in anaerobic sulfate-rich reactors

The identification of dominant microbes in anaerobic mercury (Hg) methylation, methylmercury (MeHg) demethylation, and methane oxidation as sulfate-reducing bacteria, methanogens or, probably, anaerobic methanotrophic archaea (ANMEs) is of great interest. To date, however, the interrelationship of bacteria and archaea involved in these processes remains unclear. Here, we demonstrated the dynamics of microorganisms participating in these processes. Anaerobic fixed-bed reactors were operated with swine manure and sludge to produce methane stably, and then, sulfate (reactor C), sulfate and Hg(II) (reactor H), and sulfate and MeHg (reactor M) were added, and the reactors were operated for 120 d, divided equally into four periods, P1-P4. The bacterial compositions changed nonsignificantly, whereas Methanosaeta in reactors H and M decreased significantly, revealing that it was irrelevant for Hg transformation. The abundances of Syntrophomonadaceae, Methanoculleus, Candidatus Methanogranum and Candidatus Methanoplasma increased continuously with time; these species probably functioned in these processes, but further evidence is needed. Desulfocella and Desulfobacterium dominated first but eventually almost vanished, while the dominant archaeal genera Methanogenium, Methanoculleus and Methanocorpusculum were closely related to ANME-1 and ANME-2. PLS-DA results indicated that both bacteria and archaea in different periods in the three reactors were clustered separately, implying that the microbial compositions in the same periods were similar and changed markedly with time.

The Archaeal Small Heat Shock Protein Hsp17.6 Protects Proteins from Oxidative Inactivation

Small heat shock proteins (sHsps) are widely distributed among various types of organisms and function in preventing the irreversible aggregation of thermal denaturing proteins. Here, we report that Hsp17.6 from Methanolobus psychrophilus exhibited protection of proteins from oxidation inactivation. The overexpression of Hsp17.6 in Escherichia coli markedly increased the stationary phase cell density and survivability in HClO and H₂O₂. Treatments with 0.2 mM HClO or 10 mM H₂O₂ reduced malate dehydrogenase (MDH) activity to 57% and 77%, whereas the addition of Hsp17.6 recovered the activity to 70-90% and 86-100%, respectively. A similar effect for superoxide dismutase oxidation was determined for Hsp17.6. Non-reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis assays determined that the Hsp17.6 addition decreased H₂O₂-caused disulfide-linking protein contents and HClO-induced degradation of MDH; meanwhile, Hsp17.6 protein appeared to be oxidized with increased molecular weights. Mass spectrometry identified oxygen atoms introduced into the larger Hsp17.6 molecules, mainly at the aspartate and methionine residues. Substitution of some aspartate residues reduced Hsp17.6 in alleviating H₂O₂- and HClO-caused MDH inactivation and in enhancing the E. coli survivability in H₂O₂ and HClO, suggesting that the archaeal Hsp17.6 oxidation protection might depend on an "oxidant sink" effect, i.e., to consume the oxidants in environments via aspartate oxidation.

Post-transcriptional regulation is involved in the cold-active methanol-based methanogenic pathway of a psychrophilic methanogen

The methanol-derived methanogenetic pathway contributes to bulk methane production in cold regions, but the cold adaptation mechanisms are obscure. This work investigated the mechanisms using a psychrophilic methylotrophic methanogen Methanolobus psychrophilus R15. R15 possesses two mtaCB operon paralogues-encoding methanol:corrinoid methyltransferase that is key to methanol-based methanogenesis. Molecular combined methanogenic assays determined that MtaC1 is important in methanogenesis at the optimal temperature of 18°C, but MtaC2 can be a cold-adaptive paralogue by highly upregulated at 8°C. The 5'P-seq and 5'RACE all assayed that processing occurred at the 5' untranslated region (5'-UTR) of mtaC2; reporter genes detected higher protein expression, and RNA half-life experiments assayed prolonged lifespan of the processed transcript. Therefore, mtaC2 5'-UTR processing to move the bulged structure elevated both the translation efficiency and transcript stability. 5'P-seq, quantitative RT-PCR and northern blot all identified enhanced mtaC2 5'-UTR processing at 8°C, which could contribute to the upregulation of mtaC2 at cold. The R15 cell extract contains an endoribonuclease cleaving an identified 10 nt-processing motif and the native mtaC2 5'-UTR particularly folded at 8°C. Therefore, this study revealed a 5'-UTR processing mediated post-transcriptional regulation mechanism controlling the cold-adaptive methanol-supported methanogenetic pathway, which may be used by other methylotrophic methanogens.

Methane emissions respond to soil temperature in convergent patterns but divergent sensitivities across wetlands along altitude

Among the global coordinated patterns in soil temperature and methane emission from wetlands, a declining trend of optimal soil temperature for methane emissions from low to high latitudes has been witnessed, while the corresponding trend along the altitudinal gradient has not yet been investigated. We therefore selected two natural wetlands located at contrasting climatic zones from foothill and mountainside of Nepal Himalayas, to test: (1) whether the optimal temperature for methane emissions decreases from low to high altitude, and (2) whether there is a difference in temperature sensitivity of methane emissions from those wetlands. We found significant spatial and temporal variation of methane emissions between the two wetlands and seasons. Soil temperature was the dominant driver for seasonal variation in methane emissions from both wetlands, though its effect was perplexed by the level of standing water, aquatic plants, and dissolved organic carbon, particularly in the deep water area. When integrative comparison was conducted by adding the existing data from wetlands of diverse altitudes, and the latitude-for-altitude effect was taken into account, we found the baseline soil temperatures decrease whilst the altitude rises with respect to a rapid increase in methane emission from all wetlands, however, remarkably higher sensitivity of methane emissions to soil temperature (apparent Q₁₀ ) was found in mid-altitude wetland. We provide the first evidence of an apparent decline in optimal temperature for methane emissions with increasing elevation. These findings suggest a convergent pattern of methane emissions with respect to seasonal temperature shifts from wetlands along altitudinal gradient, while a divergent pattern in temperature sensitivities exhibits a single peak in mid-altitude.

Combination of H2SO4-acidification and temperature-decrease for eco-friendly storage of pig slurry

Owing to the economic benefit and efficiency, H₂SO₄-acidification is often applied for reducing CH₄ emissions during storage of pig slurry (PS). However, it encounters with several problems related with safety and the concomitant H₂S emissions. To reduce the required amount of H₂SO₄, in this study, the storage at low temperature (20-35 °C) was applied to the mild-acidified PS (pH 6.5 and 7.0). 55.1 kg CO₂ eq./ton PS of CH₄ was emitted from the control (non-acidified at 35 °C), which was reduced to 14.4-40.2 kg CO₂ eq./ton PS at 20-30 °C. Temperature-decrease led to the increase of the abundance of methanogens (Methanobrevibacter and Methanolobus) that can grow at low temperature and the drop of specific methanogenic activity value. To achieve 70 % CH₄ reduction, 1.6 kg H₂SO₄/ton PS was needed in PS acidification, which was decreased to 0.5 kg H₂SO₄/ton PS by decreasing temperature from 35 °C to 25 °C. CH₄ production potential of the PS stored at 35 °C-pH 6.5 and 25 °C-pH 7.0 was increased by 21-33 % compared to the control. The GHG reduction of 33.6-41.9 kg CO₂ eq./ton PS and the profit of 6.6 USD/ton PS could be attained by applying acidification or combined storage, indicating that the temperature-decrease can be effectively combined with H₂SO₄-acidification.

Methanogenic archaea in peatlands

Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.

Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia

A halotolerant, psychrotolerant and methylotrophic methanogen, strain SY-01^T, was isolated from the saline Lake Tus in Siberia. Cells of strain SY-01^T were non-motile, cocci and 0.8-1.0 µm in diameter. The only methanogenic substrate utilized by strain SY-01^T was methanol. The temperature range of growth for strain SY-01^T was from 4 to 40 °C and the optimal temperature for growth was 30 °C. The pH range of growth was from pH 7.2 to 9.0, with optimal growth at pH 8.0. The NaCl range of growth was 0-1.55 M with optimal growth at 0.51 M NaCl. The G+C content of the genome of strain SY-01^T was 43.6 mol % as determined by genome sequencing. Phylogenetic analysis revealed that strain SY-01^T was most closely related to Methanolobus zinderi SD1^T (97.3 % 16S rRNA gene sequence similarity), and had 95.5-97.2 % similarities to other Methanolobus species with valid names. Genome relatedness between strain SY-01^T and DSM 21339^T was computed using average nucleotide identity and digital DNA-DNAhybridization, which yielded values of 79.7 and 21.7 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01^T represents a novel species of the genus Methanolobus, and the name Methanolobus halotolerans sp. nov. is proposed. The type strain is SY-01^T (=BCRC AR10051^T=NBRC 113166 ^T=DSM 107642^T).

Effects of Organic Phosphorus on Methylotrophic Methanogenesis in Coastal Lagoon Sediments With Seagrass (Zostera marina) Colonization

Methanogens are the major contributors of greenhouse gas methane and play significant roles in the degradation and transformation of organic matter. These organisms are particularly abundant in Swan Lake, which is a shallow lagoon located in Rongcheng Bay, Yellow Sea, northern China, where eutrophication from overfertilization commonly results in anoxic environments. High organic phosphorus content is a key component of the total phosphorus in Swan Lake and is possibly a key factor affecting the eutrophication and carbon and nitrogen cycling in Swan Lake. The effects of organic phosphorus on eutrophication have been well-studied with respect to bacteria, such as cyanobacteria, unlike the effects of organic phosphorus on methanogenesis. In this study, different sediment layer samples of seagrass-vegetated and unvegetated areas in Swan Lake were investigated to understand the effects of organic phosphorus on methylotrophic methanogenesis. The results showed that phytate phosphorus significantly promoted methane production in the deepest sediment layer of vegetated regions but suppressed it in unvegetated regions. Amplicon sequencing revealed that methylotrophic Methanococcoides actively dominated in all enrichment samples from both regions with additions of trimethylamine or phytate phosphorus, whereas methylotrophic Methanolobus and Methanosarcina predominated in the enrichments obtained from vegetated and unvegetated sediments, respectively. These results prompted further study of the effects of phytate phosphorus on two methanogen isolates, Methanolobus psychrophilus, a type strain, Methanosarcina mazei, an isolate from Swan Lake sediments. Cultivation experiments showed that phytate phosphorus could inhibit methane production by M. psychrophilus but promote methane production by M. mazei. These culture-based studies revealed the effects of organic phosphorus on methylotrophic methanogenesis in coastal lagoon sediments and improves our understanding of the mechanisms of organic carbon cycling leading to methanogenesis mediated by organic phosphorus dynamics in coastal wetlands.

Effects of storage temperature on CH4 emissions from cattle manure and subsequent biogas production potential

CH₄ is one of the main greenhouse gases (GHGs) generated from agricultural sector, and a significant amount of it is emitted during the storage of livestock manure. To mitigate the CH₄ emissions, strong acid addition to the manure was attempted, which is only applicable to slurry-type manure. On the other hand, lowering the storage temperature could be an effective method to reduce the CH₄ emissions, particularly applicable to solid-type manure. In this study, cattle manure (CM) with a high-solid content (TS > 30%) was stored at different temperatures (15-35 °C) for 80 d. The highest CH₄ emissions of 375.1 kg CO₂ eq./ton VS was observed at 35 °C, and this was reduced to less than half at ≤20 °C. Like the difference in CH₄ emissions, the degradation of organic matter showed a similar trend. The maximum VS reduction of 29% was observed at 35 °C, while only 8% reduction was observed at 15 °C. Results from microbial community analyses and specific methanogenic activity tests indicated that hydrogenotrophic methanogens were the dominant indigenous CH₄-producers, and the abundance of psychrophilic methanogens increased with decreasing temperature. The conservation of organic matter at low temperature led to an increase in biogas production potential from 25 to 43 L CH₄/kg CM. It was calculated that the GHGs emissions from electricity consumption for cooling CM below 25 °C can be offset by mitigating CH₄ emissions during storage but increasing in subsequent biogas production potential of CM. Compared at 35 °C, 91.6 kg CO₂ eq./ton CM of GHGs reduction can be attained at 15 °C.

Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils

Understanding the sources and controls on microbial methane production from wetland soils is critical to global methane emission predictions, particularly in light of changing climatic conditions. Current biogeochemical models of methanogenesis consider only acetoclastic and hydrogenotrophic sources and exclude methylotrophic methanogenesis, potentially underestimating microbial contributions to methane flux. Our multi-omic results demonstrated that methylotrophic methanogens of the family Methanomassiliicoccaceae were present and active in a freshwater wetland, with metatranscripts indicating that methanol, not methylamines, was the likely substrate under the conditions measured here. However, laboratory experiments indicated the potential for other methanogens to become enriched in response to trimethylamine, revealing the reservoir of methylotrophic methanogenesis potential residing in these soils. Collectively, our approach used coupled field and laboratory investigations to illuminate metabolisms influencing the terrestrial microbial methane cycle, thereby offering direction for increased realism in predictive process-oriented models of methane flux in wetland soils.

Wetland soils are one of the largest natural contributors to the emission of methane, a potent greenhouse gas. Currently, microbial contributions to methane emissions from these systems emphasize the roles of acetoclastic and hydrogenotrophic methanogens, while less frequently considering methyl-group substrates (e.g., methanol and methylamines). Here, we integrated laboratory and field experiments to explore the potential for methylotrophic methanogenesis in Old Woman Creek (OWC), a temperate freshwater wetland located in Ohio, USA. We first demonstrated the capacity for methylotrophic methanogenesis in these soils using laboratory soil microcosms amended with trimethylamine. However, subsequent field porewater nuclear magnetic resonance (NMR) analyses to identify methanogenic substrates failed to detect evidence for methylamine compounds in soil porewaters, instead noting the presence of the methylotrophic substrate methanol. Accordingly, our wetland soil-derived metatranscriptomic data indicated that methanol utilization by the Methanomassiliicoccaceae was the likely source of methylotrophic methanogenesis. Methanomassiliicoccaceae relative contributions to mcrA transcripts nearly doubled with depth, accounting for up to 8% of the mcrA transcripts in 25-cm-deep soils. Longitudinal 16S rRNA amplicon and mcrA gene surveys demonstrated that Methanomassiliicoccaceae were stably present over 2 years across lateral and depth gradients in this wetland. Meta-analysis of 16S rRNA sequences similar (>99%) to OWC Methanomassiliicoccaceae in public databases revealed a global distribution, with a high representation in terrestrial soils and sediments. Together, our results demonstrate that methylotrophic methanogenesis likely contributes to methane flux from climatically relevant wetland soils.

IMPORTANCE Understanding the sources and controls on microbial methane production from wetland soils is critical to global methane emission predictions, particularly in light of changing climatic conditions. Current biogeochemical models of methanogenesis consider only acetoclastic and hydrogenotrophic sources and exclude methylotrophic methanogenesis, potentially underestimating microbial contributions to methane flux. Our multi-omic results demonstrated that methylotrophic methanogens of the family Methanomassiliicoccaceae were present and active in a freshwater wetland, with metatranscripts indicating that methanol, not methylamines, was the likely substrate under the conditions measured here. However, laboratory experiments indicated the potential for other methanogens to become enriched in response to trimethylamine, revealing the reservoir of methylotrophic methanogenesis potential residing in these soils. Collectively, our approach used coupled field and laboratory investigations to illuminate metabolisms influencing the terrestrial microbial methane cycle, thereby offering direction for increased realism in predictive process-oriented models of methane flux in wetland soils.

Pattern of microbial community composition and functional gene repertoire associated with methane emission from Zoige wetlands, China-A review

The Hindu-Kush Himalaya region extends over 4 million km² across the eight countries. Knowingly, the Qinghai-Tibetan Plateau (QTP) is considered the principal altitudinal permafrost constituent on earth and is deemed as the third 'pole'. Among which, the Zoige wetlands are located in the northeastern boundary of QTP, wrapping a total area of 6180 km² with an average altitude of 3500 m. This entire region is the hotspot for methane emission since the last decade. Given the importance of methane emission, many studies have focused on the effect of environmental fluctuations on the overall methane profile and, more recently on the methanogenic community structure. The current review summarizes recent advancements of the methanogenic community and methane profile and outlines a framework for better understanding of the microbial ecology of the Zoige wetlands, China. Moreover, as microorganisms are indispensable to biogeochemical cycles, especially for methane, they are believed to be the best indicators to identify the condition of wetlands. Hence, we suggest that, underpinning the microbial profile could help understand the status of a wetland.

Enhanced glycosylation of an S-layer protein enables a psychrophilic methanogenic archaeon to adapt to elevated temperatures in abundant substrates

Adaptation to higher temperatures would increase the environmental competitiveness of psychrophiles, organisms that thrive in low-temperature environments. Methanolobus psychrophilus, a cold wetland methanogen, 'evolved' as a mesophile, growing optimally at 30 °C after subculturings, and cells grown with ample substrates exhibited higher integrity. Here, we investigated N-glycosylation of S-layer proteins, the major archaeal envelope component, with respect to mesophilic adaptation. Lectin affinity enriched a glycoprotein in cells grown at 30 °C under ample substrate availability, which was identified as the S-layer protein Mpsy_1486. Four N-glycosylation sites were identified on Mpsy_1486, which exhibited different glycosylation profiles, with N94 only found in cells cultured at 30 °C. An N-linked glycosylation inhibitor, tunicamycin, reduced glycosylation levels of Mpsy_1486 and growth at 30 °C, thus establishing a link between S-layer protein glycosylation and higher temperature adaptation of the psychrophilic archaeon M. psychrophilus.

Extreme environments: microbiology leading to specialized metabolites

The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.

The acetotrophic pathway dominates methane production in Zoige alpine wetland coexisting with hydrogenotrophic pathway

As a typical alpine wetland on the Tibetan Plateau, the Zoige wetland processes a large carbon stock and is a hotspot of methane emission. To date, many studies have investigated the methane flux in this wetland; however, the research on the source of methane in the soils of Zoige wetland is not clear enough. In this study, we determined the dynamic characteristics of the stable carbon isotopes during the methanogenesis of Zoige wetland soil and the corresponding microbial changes. The results showed that the δ¹³CH₄ varied between −19.86‰ and −28.32‰ and the α_C ranged from 1.0029 to 1.0104 in the methanogenesis process, which suggests the dominance of acetotrophic methanogenesis. And among the increased methanogens, acetotrophic methanogens multiplied more obviously than hydrogenotrophic menthanogens. In addition, the results of structural equation models showed that the variations in stable carbon isotopes during the process were mainly affected by acetotrophic methanogens. Although the acetotrophic pathway was dominate, the varied isotope characteristics, increased methanogens and ratio of carbon dioxide to methane all showed that hydrogenotrophic and acetotrophic methanogenesis coexisted in the Zoige wetland. Overall, our study provided a detailed and definitive information to the source of methane in the soil of the Zoige wetland and laid a foundation of mechanism to the research of greenhouse gas in this alpine wetland.

Rare Biosphere Archaea Assimilate Acetate in Precambrian Terrestrial Subsurface at 2.2 km Depth

The deep biosphere contains a large portion of the total microbial communities on Earth, but little is known about the carbon sources that support deep life. In this study, we used Stable Isotope Probing (SIP) and high throughput amplicon sequencing to identify the acetate assimilating microbial communities at 2260 m depth in the bedrock of Outokumpu, Finland. The long-term and short-term effects of acetate on the microbial communities were assessed by DNA-targeted SIP and RNA targeted cell activation. The microbial communities reacted within hours to the amended acetate. Archaeal taxa representing the rare biosphere at 2260 m depth were identified and linked to the cycling of acetate, and were shown to have an impact on the functions and activity of the microbial communities in general through small key carbon compounds. The major archaeal lineages identified to assimilate acetate and metabolites derived from the labelled acetate were Methanosarcina spp., Methanococcus spp., Methanolobus spp., and unclassified Methanosarcinaceae. These archaea have previously been detected in the Outokumpu deep subsurface as minor groups. Nevertheless, their involvement in the assimilation of acetate and secretion of metabolites derived from acetate indicated an important role in the supporting of the whole community in the deep subsurface, where carbon sources are limited.

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.

Methanogens: biochemical background and biotechnological applications

Since fossil sources for fuel and platform chemicals will become limited in the near future, it is important to develop new concepts for energy supply and production of basic reagents for chemical industry. One alternative to crude oil and fossil natural gas could be the biological conversion of CO2 or small organic molecules to methane via methanogenic archaea. This process has been known from biogas plants, but recently, new insights into the methanogenic metabolism, technical optimizations and new technology combinations were gained, which would allow moving beyond the mere conversion of biomass. In biogas plants, steps have been undertaken to increase yield and purity of the biogas, such as addition of hydrogen or metal granulate. Furthermore, the integration of electrodes led to the development of microbial electrosynthesis (MES). The idea behind this technique is to use CO2 and electrical power to generate methane via the microbial metabolism. This review summarizes the biochemical and metabolic background of methanogenesis as well as the latest technical applications of methanogens. As a result, it shall give a sufficient overview over the topic to both, biologists and engineers handling biological or bioelectrochemical methanogenesis.

Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems

About half of the global methane (CH₄ ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH₄ emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.

Conserved TRAM Domain Functions as an Archaeal Cold Shock Protein via RNA Chaperone Activity

Cold shock proteins (Csps) enable organisms to acclimate to and survive in cold environments and the bacterial CspA family exerts the cold protection via its RNA chaperone activity. However, most Archaea do not contain orthologs to the bacterial csp. TRAM, a conserved domain among RNA modification proteins ubiquitously distributed in organisms, occurs as an individual protein in most archaeal phyla and has a structural similarity to Csp proteins, yet its biological functions remain unknown. Through physiological and biochemical studies on four TRAM proteins from a cold adaptive archaeon Methanolobus psychrophilus R15, this work demonstrated that TRAM is an archaeal Csp and exhibits RNA chaperone activity. Three TRAM encoding genes (Mpsy_0643, Mpsy_3043, and Mpsy_3066) exhibited remarkable cold-shock induced transcription and were preferentially translated at lower temperature (18°C), while the fourth (Mpsy_2002) was constitutively expressed. They were all able to complement the cspABGE mutant of Escherichia coli BX04 that does not grow in cold temperatures and showed transcriptional antitermination. TRAM3066 (gene product of Mpsy_3066) and TRAM2002 (gene product of Mpsy_2002) displayed sequence-non-specific RNA but not DNA binding activity, and TRAM3066 assisted RNases in degradation of structured RNA, thus validating the RNA chaperone activity of TRAMs. Given the chaperone activity, TRAM is predicted to function beyond a Csp.

Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens

Extracellular capsules constitute the outermost layer of many bacteria, are major virulence factors, and affect antimicrobial therapies. They have been used as epidemiological markers and recently became vaccination targets. Despite the efforts to biochemically serotype capsules in a few model pathogens, little is known of their taxonomic and environmental distribution. We developed, validated, and made available a computational tool, CapsuleFinder, to identify capsules in genomes. The analysis of over 2500 prokaryotic genomes, accessible in a database, revealed that ca. 50% of them—including Archaea—encode a capsule. The Wzx/Wzy-dependent capsular group was by far the most abundant. Surprisingly, a fifth of the genomes encode more than one capsule system—often from different groups—and their non-random co-occurrence suggests the existence of negative and positive epistatic interactions. To understand the role of multiple capsules, we queried more than 6700 metagenomes for the presence of species encoding capsules and showed that their distribution varied between environmental categories and, within the human microbiome, between body locations. Species encoding capsules, and especially those encoding multiple capsules, had larger environmental breadths than the other species. Accordingly, capsules were more frequent in environmental bacteria than in pathogens and, within the latter, they were more frequent among facultative pathogens. Nevertheless, capsules were frequent in clinical samples, and were usually associated with fast-growing bacteria with high infectious doses. Our results suggest that capsules increase the environmental range of bacteria and make them more resilient to environmental perturbations. Capsules might allow opportunistic pathogens to profit from empty ecological niches or environmental perturbations, such as those resulting from antibiotic therapy, to colonize the host. Capsule-associated virulence might thus be a by-product of environmental adaptation. Understanding the role of capsules in natural environments might enlighten their function in pathogenesis.

Extracellular capsules protect bacterial cells from external aggressions such as antibiotics or desiccation, but can also be targeted by vaccines. Since little was known about their frequency across Prokaryotes, we created and made freely available a computational tool, CapsuleFinder, to identify them from genomic data. Surprisingly, its use showed that many bacterial strains, especially those with the largest genomes, encode several capsules. The frequencies of the different combinations of capsule groups depended strongly on the phyla and the groups themselves, suggesting the existence of epistatic interactions between capsules. Bacteria encoding capsule systems were found in many natural environments, and were frequent in the human microbiome. In contrast to their frequent association with virulence, we found many more capsules in non-pathogens or facultative pathogens than among obligatory pathogens. We suggest that capsules increase the environmental breadth of bacteria thereby facilitating host colonization by opportunistic pathogens.

Reduction of Methane Emission during Slurry Storage by the Addition of Effective Microorganisms and Excessive Carbon Source from Brewing Sugar

Storing livestock manure is the primary stage of manure management where microbial processes and chemical reactions result in the release of methane (CH), nitrous oxide (NO), ammonia (NH), and carbon dioxide (CO). This study examined the reduction of CH emissions from slurry storage under two temperatures (cool [10°C] and warm [30°C]) when a glucose-rich substrate (brewing sugar) and activated effective microorganisms were applied at 10% (w/w) and 5% (v/w), respectively. Brewing sugar addition influenced microbial anaerobic respiration, resulting in a reduction of slurry pH to <5.0, through "self-acidification" caused by lactic acid production. Subsequently, CH emissions were significantly reduced by 87 and 99% in the cool and warm environments, respectively. The effective microorganism treatment did not change the chemical characteristics of the slurry but reduced CH emissions by 17 and 27% ( < 0.05) in the cool and warm environments, respectively. These results suggest that self-acidification after addition of a carbon source may be a promising alternative to slurry acidification using concentrated acids.

Biologically Produced Methane as a Renewable Energy Source

Methanogens are a unique group of strictly anaerobic archaea that are more metabolically diverse than previously thought. Traditionally, it was thought that methanogens could only generate methane by coupling the oxidation of products formed by fermentative bacteria with the reduction of CO₂. However, it has recently been observed that many methanogens can also use electrons extruded from metal-respiring bacteria, biocathodes, or insoluble electron shuttles as energy sources. Methanogens are found in both human-made and natural environments and are responsible for the production of ∼71% of the global atmospheric methane. Their habitats range from the human digestive tract to hydrothermal vents. Although biologically produced methane can negatively impact the environment if released into the atmosphere, when captured, it can serve as a potent fuel source. The anaerobic digestion of wastes such as animal manure, human sewage, or food waste produces biogas which is composed of ∼60% methane. Methane from biogas can be cleaned to yield purified methane (biomethane) that can be readily incorporated into natural gas pipelines making it a promising renewable energy source. Conventional anaerobic digestion is limited by long retention times, low organics removal efficiencies, and low biogas production rates. Therefore, many studies are being conducted to improve the anaerobic digestion process. Researchers have found that addition of conductive materials and/or electrically active cathodes to anaerobic digesters can stimulate the digestion process and increase methane content of biogas. It is hoped that optimization of anaerobic digesters will make biogas more readily accessible to the average person.

Anaerobic oxidation of methane associated with sulfate reduction in a natural freshwater gas source

The occurrence of anaerobic oxidation of methane (AOM) and trace methane oxidation (TMO) was investigated in a freshwater natural gas source. Sediment samples were taken and analyzed for potential electron acceptors coupled to AOM. Long-term incubations with ¹³C-labeled CH₄ (¹³CH₄) and different electron acceptors showed that both AOM and TMO occurred. In most conditions, ¹³C-labeled CO₂ (¹³CO₂) simultaneously increased with methane formation, which is typical for TMO. In the presence of nitrate, neither methane formation nor methane oxidation occurred. Net AOM was measured only with sulfate as electron acceptor. Here, sulfide production occurred simultaneously with ¹³CO₂ production and no methanogenesis occurred, excluding TMO as a possible source for ¹³CO₂ production from ¹³CH₄. Archaeal 16S rRNA gene analysis showed the highest presence of ANME-2a/b (ANaerobic MEthane oxidizing archaea) and AAA (AOM Associated Archaea) sequences in the incubations with methane and sulfate as compared with only methane addition. Higher abundance of ANME-2a/b in incubations with methane and sulfate as compared with only sulfate addition was shown by qPCR analysis. Bacterial 16S rRNA gene analysis showed the presence of sulfate-reducing bacteria belonging to SEEP-SRB1. This is the first report that explicitly shows that AOM is associated with sulfate reduction in an enrichment culture of ANME-2a/b and AAA methanotrophs and SEEP-SRB1 sulfate reducers from a low-saline environment.

Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies

Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens.

The seasonal variation of emission of greenhouse gases from a full-scale sewage treatment plant

The seasonal variety of greenhouse gas (GHGs) emissions and the main emission source in a sewage treatment plant were investigated. The emission coefficient to treated wastewater was 291gCO2m(-3). The main source of GHGs was CO2 from the consumption of electricity, nitrous oxide from the sludge incineration process, and methane from the water treatment process. They accounted for 43.4%, 41.7% and 8.3% of the total amount of GHGs emissions, respectively. The amount of methane was plotted as a function of water temperature ranging between 13.3 and 27.3°C. An aeration tank was the main source of methane emission from all the units. Almost all the methane was emitted from the aeration tank, which accounted for 86.4% of the total gaseous methane emission. However, 18.4% of the methane was produced in sewage lines, 15.4% in the primary sedimentation tank, and 60.0% in the aeration tank.

Average oxidation state of carbon in proteins

The formal oxidation state of carbon atoms in organic molecules depends on the covalent structure. In proteins, the average oxidation state of carbon (Z(C)) can be calculated as an elemental ratio from the chemical formula. To investigate oxidation-reduction (redox) patterns, groups of proteins from different subcellular locations and phylogenetic groups were selected for comparison. Extracellular proteins of yeast have a relatively high oxidation state of carbon, corresponding with oxidizing conditions outside of the cell. However, an inverse relationship between Z(C) and redox potential occurs between the endoplasmic reticulum and cytoplasm. This trend provides support for the hypothesis that protein transport and turnover are ultimately coupled to the maintenance of different glutathione redox potentials in subcellular compartments. There are broad changes in Z(C) in whole-genome protein compositions in microbes from different environments, and in Rubisco homologues, lower Z(C) tends to occur in organisms with higher optimal growth temperature. Energetic costs calculated from thermodynamic models are consistent with the notion that thermophilic organisms exhibit molecular adaptation to not only high temperature but also the reducing nature of many hydrothermal fluids. Further characterization of the material requirements of protein metabolism in terms of the chemical conditions of cells and environments may help to reveal other linkages among biochemical processes with implications for changes on evolutionary time scales.

The microbial diversity, distribution, and ecology of permafrost in China: a review

Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

Methanol induces low temperature resilient methanogens and improves methane generation from domestic wastewater at low to moderate temperatures

Low temperature (<20 °C) limits bio-methanation of sewage. Literature shows that hydrogenotrophic methanogens can adapt themselves to low temperature and methanol is a preferred substrate by methanogens in cold habitats. The study hypothesizes that methanol can induce the growth of low-temperature resilient, methanol utilizing, hydrogenotrophs in UASB reactor. The hypothesis was tested in field conditions to evaluate the impact of seasonal temperature variations on methane yield in the presence and absence of methanol. Results show that 0.04% (v/v) methanol increased methane up to 15 times and its effect was more pronounced at lower temperatures. The qPCR analysis showed the presence of Methanobacteriales along with Methanosetaceae in large numbers. This indicates methanol induced the growth of both the hydrogenotrophic and acetoclastic groups through direct and indirect routes, respectively. This study thus demonstrated that methanol can impart resistance in methanogenic biomass to low temperature and can improve performance of UASB reactor.

Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus

Psychrophilic methanogenic Archaea contribute significantly to global methane emissions, but archaeal cold adaptation mechanisms remain poorly understood. Hinted by that mRNA architecture determined secondary structure respond to cold more promptly than proteins, differential RNA-seq was used in this work to examine the genome-wide transcription start sites (TSSs) of the psychrophilic methanogen Methanolobus psychrophilus R15 and its response to cold. Unlike most prokaryotic mRNAs with short 5' untranslated regions (5' UTR, median lengths of 20-40 nt), 51% mRNAs of this methanogen have large 5' UTR (>50 nt). For 24% of the mRNAs, the 5' UTR is >150 nt. This implies that post-transcriptional regulation may be significance in the psychrophile. Remarkably, 219 (14%) genes possessed multiple gene TSSs (gTSSs), and 84 genes exhibited temperature-regulated gTSS selection to express alternative 5' UTR. Primer extension studies confirmed the temperature-dependent TSS selection and a stem-loop masking of ribosome binding sites was predicted from the longer 5' UTRs, suggesting alternative 5' UTRs-mediated translation regulation in the cold adaptation as well. In addition, 195 small RNAs (sRNAs) were detected, and Northern blots confirmed that many sRNAs were induced by cold. Thus, this study revealed an integrated transcriptional and post-transcriptional regulation for cold adaptation in a psychrophilic methanogen.

Snapshot of methanogen sensitivity to temperature in Zoige wetland from Tibetan plateau

Zoige wetland in Tibetan plateau represents a cold environment at high altitude where significant methane emission has been observed. However, it remains unknown how the production and emission of CH₄ from Zoige wetland will respond to a warming climate. Here we investigated the temperature sensitivity of methanogen community in a Zoige wetland soil under the laboratory incubation conditions. One soil sample was collected and the temperature sensitivity of the methanogenic activity, the structure of methanogen community and the methanogenic pathways were determined. We found that the response of methanogenesis to temperature could be separated into two phases, a high sensitivity in the low temperature range and a modest sensitivity under mesophilic conditions, respectively. The aceticlastic methanogens Methanosarcinaceae were the main methanogens at low temperatures, while hydrogenotrophic Methanobacteriales, Methanomicrobiales, and Methanocellales were more abundant at higher temperatures. The total abundance of mcrA genes increased with temperature indicating that the growth of methanogens was stimulated. The growth of hydrogenotrophic methanogens, however, was faster than aceticlastic ones resulting in the shift of methanogen community. Determination of carbon isotopic signatures indicated that methanogenic pathway was also shifted from mainly aceticlastic methanogenesis to a mixture of hydrogenotrophic and aceticlastic methanogenesis with the increase of temperature. Collectively, the shift of temperature responses of methanogenesis was in accordance with the changes in methanogen composition and methanogenic pathway in this wetland sample. It appears that the aceticlastic methanogenesis dominating at low temperatures is more sensitive than the hydrogenotrophic one at higher temperatures.

Bacterial and archaeal communities in Lake Nyos (Cameroon, Central Africa)

The aim of this study was to assess the microbial diversity associated with Lake Nyos, a lake with an unusual chemistry in Cameroon. Water samples were collected during the dry season on March 2013. Bacterial and archaeal communities were profiled using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) approach of the 16S rRNA gene. The results indicate a stratification of both communities along the water column. Altogether, the physico-chemical data and microbial sequences suggest a close correspondence of the potential microbial functions to the physico-chemical pattern of the lake. We also obtained evidence of a rich microbial diversity likely to include several novel microorganisms of environmental importance in the large unexplored microbial reservoir of Lake Nyos.

Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature

A psychrotolerant hydrogenotrophic methanogen, strain Pt1, was isolated from a syntrophic propionate-oxidizing methanogenic consortium obtained from granulated biomass of a two-stage low-temperature (3–8 °C) anaerobic expanded granular sludge bed (EGSB) bioreactor, fed with a mixture of volatile fatty acids (VFAs) (acetate, propionate and butyrate). The strain was strictly anaerobic, and cells were curved rods, 0.4–0.5×7.5–25 µm, that sometimes formed wavy filaments from 25 to several hundred micrometres in length. Cells stained Gram-negative and were non-sporulating. They were gently motile by means of tufted flagella. The strain grew at 5–37 °C (optimum at 20–30 °C), at pH 6.0–10 (optimum 7.0–7.5) and with 0–0.3 M NaCl (optimum 0 M NaCl). Growth and methane production was found with H2/CO2 and very weak growth with formate. Acetate and yeast extract stimulated growth, but were not essential. The G+C content of the DNA of strain Pt1 was 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Pt1 was a member of the genus Methanospirillum and showed 97.5 % sequence similarity to Methanospirillum hungatei JF1T and 94 % sequence similarity to Methanospirillum lacunae Ki8-1T. DNA–DNA hybridization of strain Pt1 with Methanospirillum hungatei JF1T revealed 39 % relatedness. On the basis of its phenotypic characteristics and phylogenetic position, strain Pt1 is a representative of a novel species of the genus Methanospirillum , for which the name Methanospirillum stamsii sp. nov. is proposed. The type strain is Pt1T ( = DSM 26304T = VKM B-2808T).