Energy conservation in the gut microbeMethanomassiliicoccus luminyensisis based on membrane‐bound ferredoxin oxidation coupled to heterodisulfide reduction

Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov

The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L-1 NaCl (optimum 0.12 mol.L-1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05T (JCM 31474T).

Evolving understanding of rumen methanogen ecophysiology

Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.

Ecology of Methanonatronarchaeia

Methanonatronarchaeia represents a deep-branching phylogenetic lineage of extremely halo(alkali)philic and moderately thermophilic methyl-reducing methanogens belonging to the phylum Halobacteriota. It includes two genera, the alkaliphilic Methanonatronarchaeum and the neutrophilic Ca. Methanohalarchaeum. The former is represented by multiple closely related pure culture isolates from hypersaline soda lakes, while the knowledge about the latter is limited to a few mixed cultures with anaerobic haloarchaea. To get more insight into the distribution and ecophysiology of this enigmatic group of extremophilic methanogens, potential activity tests and enrichment cultivation with different substrates and at different conditions were performed with anaerobic sediment slurries from various hypersaline lakes in Russia. Methanonatronarchaeum proliferated exclusively in hypersaline soda lake samples mostly at elevated temperature, while at mesophilic conditions it coexisted with the extremely salt-tolerant methylotroph Methanosalsum natronophilum. Methanonatronarchaeum was also able to serve as a methylotrophic or hydrogenotrophic partner in several thermophilic enrichment cultures with fermentative bacteria. Ca. Methanohalarchaeum did not proliferate at mesophilic conditions and at thermophilic conditions it competed with extremely halophilic and moderately thermophilic methylotroph Methanohalobium, which it outcompeted at a combination of elevated temperature and methyl-reducing conditions. Overall, the results demonstrated that Methanonatronarchaeia are specialized extremophiles specifically proliferating in conditions of elevated temperature coupled with extreme salinity and simultaneous availability of a wide range of C₁ -methylated compounds and H₂ /formate.

Diversity and Evolution of Methane-Related Pathways in Archaea

Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase (Mcr) complex. Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Archaeal key-residents within the human microbiome: characteristics, interactions and involvement in health and disease

Since the introduction of Archaea as new domain of life more than 40 years ago, they are no longer regarded as eccentric inhabitants of extreme ecosystems. These microorganisms are widespread in various moderate ecosystems, including eukaryotic hosts such as humans. Indeed, members of the archaeal community are now recognized as paramount constituents of human microbiome, while their definite role in disease or health is not fully elucidated and no archaeal pathogen has been reported. Here, we present a brief overview of archaea residing in and on the human body, with a specific focus on common lineages including Methanobrevibacter, Methanosphaeraand Methanomassilococcales.

Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes

The KTK 4A-related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%-33.0%) within a Chinese soda-saline lake using culture-independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single-copy proteins and genome-level identity analyses among the metagenome-assembled genomes demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favourable 'salt-in' strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC-mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC-MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales. Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials and evolutional significance of Ca. Haloplasmatales.

Bioaugmentation with a propionate-degrading methanogenic culture to improve methane production from chicken manure

Volatile fatty acid (VFA) accumulation caused by high ammonia concentrations is often encountered during the anaerobic digestion (AD) of ammonia-rich substrates. In this study, propionate-degrading methanogenic cultures were introduced to augment the semi-continuous AD of chicken manure under high ammonia levels. Introduction of a methanogenic culture enhanced the methane yield in the bioaugmented digester by 17-26% when the organic loading rate (OLR) was 2-4 g L^-1d^-1 compared to that in the control. When the OLR was further increased from 4.0 L^-1d^-1 to 5.0 g L^-1d^-1, and bioaugmentation ceased, methane yield improved by 15-18% under a high total ammonia nitrogen level of 5.0-8.4 g NH₄⁺-N/L. Moreover, bioaugmentation reconstructed the methanogenic community in the digester, promoting the dominance of hydrogenotrophic Methanobacterium and slightly increasing the abundance of aceticlastic Methanothrix and the syntrophic propionate-oxidizing bacteria Syntrophobacter, which were the key contributors to the improved AD under high ammonia concentrations.

Neonicotinoids stimulate H2-limited methane emission in Periplaneta americana through the regulation of gut bacterium community

Methane emitted by insects is considered to be an important source of atmospheric methane. Here we report the stimulation of methane emission in the cockroach Periplaneta americana and termite Coptotermes chaohuensis, insects with abundant methanogens, by neonicotinoids, insecticides widely used to control insect pests. Cycloxaprid (CYC) and imidacloprid (IMI) caused foregut expansion in P. americana, and increased the methane emission. Antibiotics mostly eliminated the effects. In P. americana guts, hydrogen levels increased and pH values decreased, which could be significantly explained by the gut bacterium community change. The proportion of several bacterium genera increased in guts following CYC treatment, and two genera from four could generate hydrogen. Hydrogen is a central intermediate in methanogenesis. All increased methanogens in both foregut and hindgut used hydrogen as electron donor to produce methane. Besides, the up-regulation of mcrA, encoding the enzyme for the final step of methanogenesis suggested the enhanced methane production ability in present methanogens. In the termite, hydrogen levels in gut and methane emission also significantly increased after neonicotinoid treatment, which was similar to the results in P. americana. In summary, neonicotinoids changed bacterium community in P. americana gut to generate more hydrogen, which then stimulated gut methanogens to produce and emit more methane. The finding raised a new concern over neonicotinoid applications, and might be a potential environmental risk associated with atmospheric methane.

Process of energy conservation in the extremely haloalkaliphilic methyl-reducing methanogen Methanonatronarchaeum thermophilum

The recently isolated methanogen Methanonatronarchaeum thermophilum is an extremely haloalkaliphilic and moderately thermophilic archaeon and belongs to the novel class Methanonatronarchaeia in the phylum Halobacteriota. The knowledge about the physiology and biochemistry of members of the class Methanonatronarchaeia is still limited. It is known that M. thermophilum performs hydrogen or formate-dependent methyl-reducing methanogenesis. Here, we show that the organism was able to grow on all tested C₁ -methylated substrates (methanol, trimethylamine, dimethylamine, monomethylamine) in combination with formate or molecular hydrogen. A temporary accumulation of intermediates (dimethylamine or/and monomethylamine) in the medium occurred during the consumption of trimethylamine or dimethylamine. The energy conservation of M. thermophilum was dependent on a respiratory chain consisting of a hydrogenase (VhoGAC), a formate dehydrogenase (FdhGHI), and a heterodisulfide reductase (HdrDE) that were well adapted to the harsh physicochemical conditions in the natural habitat. The experiments revealed the presence of two variants of energy-conserving oxidoreductase systems in the membrane. These included the H₂ : heterodisulfide oxidoreductase system, which has already been described in Methanosarcina species, as well as the novel formate: heterodisulfide oxidoreductase system. The latter electron transport chain, which was experimentally proven for the first time, distinguishes the organism from all other known methanogenic archaea and represents a unique feature of the class Methanonatronarchaeia. Experiments with 2-hydroxyphenazine and the inhibitor diphenyleneiodonium chloride indicated that a methanophenazine-like cofactor might function as an electron carrier between the hydrogenase/ formate dehydrogenase and the heterodisulfide reductase.

The hydrogen threshold of obligately methyl-reducing methanogens

Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures < 0.1 Pa, which is almost one order of magnitude lower than the thresholds for M. stadtmanae and M. blatticola reported in the only previous study on this topic. We conclude that methylotrophic methanogens should outcompete hydrogenotrophic methanogens for hydrogen and that their activity is limited by the availability of methyl groups.

Functional diversity of prokaryotic HdrA(BC) modules: Role in flavin-based electron bifurcation processes and beyond

In methanogenic archaea, the archetypical complex of heterodisulfide reductase (HdrABC) and hydrogenase (MvhAGD) couples the endergonic reduction of CO₂ by H₂ to the exergonic reduction of the CoB-S-S-CoM heterodisulfide by H₂ via flavin-based electron bifurcation. Presently known enzymes containing HdrA(BC)-like components play key roles in methanogenesis, acetogenesis, respiratory sulfate reduction, lithotrophic reduced sulfur compound oxidation, aromatic compound degradation, fermentations, and probably many further processes. This functional diversity is achieved by a modular architecture of HdrA(BC) enzymes, where a big variety of electron input/output modules may be connected either directly or via adaptor modules to the HdrA(BC) components. Many, but not all HdrA(BC) complexes are proposed to catalyse a flavin-based electron bifurcation/confurcation. Despite the availability of HdrA(BC) crystal structures, fundamental questions of electron transfer and energy coupling processes remain. Here, we address the common properties and functional diversity of HdrA(BC) core modules integrated into electron-transfer machineries of outstanding complexity.

New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus 'Methanomassiliicoccus armoricus MXMAG1'. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades ('free-living'/non-host-associated environmental clade and 'host-associated'/digestive clade) allowed us to explore the putative physiological traits of Candidatus 'M. armoricus MXMAG1'. As expected, Ca. 'Methanomassiliicoccus armoricus MXMAG1' had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the 'free-living' clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.

Several ways one goal-methanogenesis from unconventional substrates

Abstract

Methane is the second most important greenhouse gas on earth. It is produced by methanogenic archaea, which play an important role in the global carbon cycle. Three main methanogenesis pathways are known: in the hydrogenotrophic pathway H₂ and carbon dioxide are used for methane production, whereas in the methylotrophic pathway small methylated carbon compounds like methanol and methylated amines are used. In the aceticlastic pathway, acetate is disproportionated to methane and carbon dioxide. However, next to these conventional substrates, further methanogenic substrates and pathways have been discovered. Several phylogenetically distinct methanogenic lineages (Methanosphaera, Methanimicrococcus, Methanomassiliicoccus, Methanonatronarchaeum) have evolved hydrogen-dependent methylotrophic methanogenesis without the ability to perform either hydrogenotrophic or methylotrophic methanogenesis. Genome analysis of the deep branching Methanonatronarchaeum revealed an interesting membrane-bound hydrogenase complex affiliated with the hardly described class 4 g of multisubunit hydrogenases possibly providing reducing equivalents for anabolism. Furthermore, methylated sulfur compounds such as methanethiol, dimethyl sulfide, and methylmercaptopropionate were described to be converted into adapted methylotrophic methanogenesis pathways of Methanosarcinales strains. Moreover, recently it has been shown that the methanogen Methermicoccus shengliensis can use methoxylated aromatic compounds in methanogenesis. Also, tertiary amines like choline (N,N,N-trimethylethanolamine) or betaine (N,N,N-trimethylglycine) have been described as substrates for methane production in Methanococcoides and Methanolobus strains. This review article will provide in-depth information on genome-guided metabolic reconstructions, physiology, and biochemistry of these unusual methanogenesis pathways.

Key points

• Newly discovered methanogenic substrates and pathways are reviewed for the first time.

• The review provides an in-depth analysis of unusual methanogenesis pathways.

• The hydrogenase complex of the deep branching Methanonatronarchaeum is analyzed.

Anaerobic co-digestion of Pennisetum hybrid and pig manure: A comparative study of performance and microbial community at different mixture ratio and organic loading rate

To investigate how the changes in performance and the microbial community of the co-digestion system of Pennisetum hybrid and pig manure, two co-digestion systems in a semi-continuous mode were established at different grass:manure mixture ratios (50:50 and 75:25), and at variable organic loading rates (OLRs). The two reactors were in a steady-state at the OLRs of 2.0-5.0 g VS/(L·d), with the specific and volumetric biogas yields of 383.86 ± 65.13 to 574.28 ± 72.04 mL/g VS and 0.87 ± 0.07 to 2.36 ± 0.13 m³/(m³·d), respectively. The co-digestion system with a mixture ratio of 75:25 failed at an OLR of 5.5 g VS/(L⋅d). This failure could be attributed to the accumulation of volatile fatty acids (VFAs) owing to the imbalance between acid-production and -oxidation bacteria. By contrast, the co-digestion system with mixture ratio of 50:50 failed at an OLR of 7.0 g VS/(L⋅d), which was likely due to mechanical issues or improper reactor configuration. The genus Proteiniphilum contributed to the increase in total ammonia nitrogen. These findings provide useful guidance for optimizing co-digestion system, enhancing reactor performance and improving the wastes treatment.

Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics

Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Most approaches to prevent the occurrence of such deleterious molecules focus on actions to interfere with gut microbiota metabolism to limit the synthesis of TMA. Some human gut archaea however use TMA as terminal electron acceptor for producing methane, thus indicating that intestinal TMA does not accumulate in some human subjects. Therefore, a rational alternative approach is to eliminate neo-synthesized intestinal TMA. This can be achieved through bioremediation of TMA by these peculiar methanogenic archaea, either by stimulating or providing them, leading to a novel kind of next-generation probiotics referred to as archaebiotics. Finally, specific components which are involved in this archaeal metabolism could also be used as intestinal TMA sequesters, facilitating TMA excretion along with stool. Referring to a standard pharmacological approach, these TMA traps could be synthesized ex vivo and then delivered into the human gut. Another approach is the engineering of known probiotic strain in order to metabolize TMA, i.e., live engineered biotherapeutic products. These alternatives would require, however, to take into account the necessity of synthesizing the 22nd amino acid pyrrolysine, i.e., some specificities of the genetics of TMA-consuming archaea. Here, we present an overview of these different strategies and recent advances in the field that will sustain such biotechnological developments. KEY POINTS: • Some autochthonous human archaea can use TMA for their essential metabolism, a methyl-dependent hydrogenotrophic methanogenesis. • They could therefore be used as next-generation probiotics for preventing some human diseases, especially cardiovascular diseases and trimethylaminuria. • Their genetic capacities can also be used to design live recombinant biotherapeutic products. • Encoding of the 22nd amino acid pyrrolysine is necessary for such alternative developments.

Methylotrophic methanogens everywhere - physiology and ecology of novel players in global methane cycling

Research on methanogenic Archaea has experienced a revival, with many novel lineages of methanogens recently being found through cultivation and suggested via metagenomics approaches, respectively. Most of these lineages comprise Archaea (potentially) capable of methanogenesis from methylated compounds, a pathway that had previously received comparably little attention. In this review, we provide an overview of these new lineages with a focus on the Methanomassiliicoccales. These lack the Wood-Ljungdahl pathway and employ a hydrogen-dependent methylotrophic methanogenesis pathway fundamentally different from traditional methylotrophic methanogens. Several archaeal candidate lineages identified through metagenomics, such as the Ca. Verstraetearchaeota and Ca. Methanofastidiosa, encode genes for a methylotrophic methanogenesis pathway similar to the Methanomassiliicoccales. Thus, the latter are emerging as a model system for physiological, biochemical and ecological studies of hydrogen-dependent methylotrophic methanogens. Methanomassiliicoccales occur in a large variety of anoxic habitats including wetlands and animal intestinal tracts, i.e. in the major natural and anthropogenic sources of methane emissions, respectively. Especially in ruminant animals, they likely are among the major methane producers. Taken together, (hydrogen-dependent) methylotrophic methanogens are much more diverse and widespread than previously thought. Considering the role of methane as potent greenhouse gas, resolving the methanogenic nature of a broad range of putative novel methylotrophic methanogens and assessing their role in methane emitting environments are pressing issues for future research on methanogens.