Identification of the Radical SAM Enzymes Involved in the Biosynthesis of Methanopterin and Coenzyme F 420 in Methanogens

Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti

Pelomyxa is a genus of anaerobic amoebae that live in consortia with multiple prokaryotic endosymbionts. Although the symbionts represent a large fraction of the cellular biomass, their metabolic roles have not been investigated. Using single-cell genomics and transcriptomics, we have characterized the prokaryotic community associated with P. schiedti, which is composed of two bacteria, Candidatus Syntrophus pelomyxae (class Deltaproteobacteria) and Candidatus Vesiculincola pelomyxae (class Clostridia), and a methanogen, Candidatus Methanoregula pelomyxae. Fluorescence in situ hybridization and electron microscopy showed that Ca. Vesiculincola pelomyxae is localized inside vesicles, whereas the other endosymbionts occur freely in the cytosol, with Ca. Methanoregula pelomyxae enriched around the nucleus. Genome and transcriptome-based reconstructions of the metabolism suggests that the cellulolytic activity of P. schiedti produces simple sugars that fuel its own metabolism and the metabolism of a Ca. Vesiculincola pelomyxae, while Ca. Syntrophus pelomyxae energy metabolism relies on degradation of butyrate and isovalerate from the environment. Both species of bacteria and the ameba use hydrogenases to transfer the electrons from reduced equivalents to hydrogen, a process that requires a low hydrogen partial pressure. This is achieved by the third endosymbiont, Ca. Methanoregula pelomyxae, which consumes H2 and formate for methanogenesis. While the bacterial symbionts can be successfully eliminated by vancomycin treatment without affecting the viability of the amoebae, treatment with 2-bromoethanesulfonate, a specific inhibitor of methanogenesis, killed the amoebae, indicating the essentiality of the methanogenesis for this consortium.

Discovery, structure, and mechanism of a tetraether lipid synthase

Archaea synthesize isoprenoid-based ether-linked membrane lipids, which enable them to withstand extreme environmental conditions, such as high temperatures, high salinity, and low or high pH values^1–5. In some archaea, such as Methanocaldococcus jannaschii, these lipids are further modified by forming carbon–carbon bonds between the termini of two lipid tails within one glycerophospholipid to generate the macrocyclic archaeol or forming two carbon–carbon bonds between the termini of two lipid tails from two glycerophospholipids to generate the macrocycle glycerol dibiphytanyl glycerol tetraether (GDGT)^1,2. GDGT contains two 40-carbon lipid chains (biphytanyl chains) that span both leaflets of the membrane, providing enhanced stability to extreme conditions. How these specialized lipids are formed has puzzled scientists for decades. The reaction necessitates the coupling of two completely inert sp³-hybridized carbon centres, which, to our knowledge, has not been observed in nature. Here we show that the gene product of mj0619 from M. jannaschii, which encodes a radical S-adenosylmethionine enzyme, is responsible for biphytanyl chain formation during synthesis of both the macrocyclic archaeol and GDGT membrane lipids⁶. Structures of the enzyme show the presence of four metallocofactors: three [Fe₄S₄] clusters and one mononuclear rubredoxin-like iron ion. In vitro mechanistic studies show that Csp³–Csp³ bond formation takes place on fully saturated archaeal lipid substrates and involves an intermediate bond between the substrate carbon and a sulfur of one of the [Fe₄S₄] clusters. Our results not only establish the biosynthetic route for tetraether formation but also improve the use of GDGT in GDGT-based paleoclimatology indices^7–10.

In Methanocaldococcus jannaschii, a radical S-adenosylmethionine enzyme catalyses the formation of the biphytanyl chain.

Contribution of periphytic biofilm of paddy soils to carbon dioxide fixation and methane emissions

Rice paddies are major contributors to anthropogenic greenhouse gas emissions via methane (CH₄) flux. The accurate quantification of CH₄ emissions from rice paddies remains problematic, in part due to uncertainties and omissions in the contribution of microbial aggregates on the soil surface to carbon fluxes. Herein, we comprehensively evaluated the contribution of one form of microbial aggregates, periphytic biofilm (PB), to carbon dioxide (CO₂) and CH₄ emissions from paddies distributed across three climatic zones, and quantified the pathways that drive net CH₄ production as well as CO₂ fixation. We found that PB accounted for 7.1%-38.5% of CH₄ emissions and 7.2%-12.7% of CO₂ fixation in the rice paddies. During their growth phase, PB fixed CO₂ and increased the redox potential, which promoted aerobic CH₄ oxidation. During the decay phase, PB degradation reduced redox potential and increased soil organic carbon availability, which promoted methanogenic microbial community growth and metabolism and increased CH₄ emissions. Overall, PB acted as a biotic converter of atmospheric CO₂ to CH₄, and aggravated carbon emissions by up to 2,318 kg CO₂ equiv ha^-1 season^-1. Our results provide proof-of-concept evidence for the discrimination of the contributions of surface microbial aggregates (i.e., PB) from soil microbes, and a profound foundation for the estimation and simulation of carbon fluxes in a potential novel approach to the mitigation of CH₄ emissions by manipulating PB growth.

Performance and microbial protein expression during anaerobic treatment of alkali-decrement wastewater using a strengthened circulation anaerobic reactor

Herein, a strengthened circulation anaerobic (SCA) reactor was employed for the treatment of actual alkali-decrement wastewater. The degradation mechanism of polyester oligomers and the relationship between the treatment performance and microbial community structure were systematically investigated using various advanced techniques. Results suggest that the accumulation of volatile fatty acids has an inhibitory effect on methanogenic activity. Molecular weight distributions suggest that only incomplete degradation of oligomers was achieved, due to acetogenic inhibition in the lower part of the SCA reactor. Meta-proteomic approach analysis revealed that the methanogens containing heterodisulfide reductase were the primary species involved in methane metabolism. Based on these findings, a possible degradation mechanism for alkali-decrement wastewater in the SCA reactor is proposed. This high-performance anaerobic reactor could be further scaled-up and optimized to serve as a promising and effective unit for the treatment of other refractory industrial wastewaters.