Transplanting the pathway engineering toolbox to methanogens

Teaching old dogs new tricks: genetic engineering methanogens

Methanogenic archaea, which are integral to global carbon and nitrogen cycling, currently face challenges in genetic manipulation due to unique physiology and limited genetic tools. This review provides a survey of current and past developments in the genetic engineering of methanogens, including selection and counterselection markers, reporter systems, shuttle vectors, mutagenesis methods, markerless genetic exchange, and gene expression control. This review discusses genetic tools and emphasizes challenges tied to tool scarcity for specific methanogenic species. Mutagenesis techniques for methanogens, including physicochemical, transposon-mediated, liposome-mediated mutagenesis, and natural transformation, are outlined, along with achievements and challenges. Markerless genetic exchange strategies, such as homologous recombination and CRISPR/Cas-mediated genome editing, are also detailed. Finally, the review concludes by examining the control of gene expression in methanogens. The information presented underscores the urgent need for refined genetic tools in archaeal research. Despite historical challenges, recent advancements, notably CRISPR-based systems, hold promise for overcoming obstacles, with implications for global health, agriculture, climate change, and environmental engineering. This comprehensive review aims to bridge existing gaps in the literature, guiding future research in the expanding field of archaeal genetic engineering.

A comprehensive review on methane's dual role: effects in climate change and potential as a carbon-neutral energy source

The unprecedented population and anthropogenic activity rise have challenged the future look up for shifts in global temperature and climate patterns. Anthropogenic activities such as land fillings, building dams, wetlands converting to lands, combustion of biomass, deforestation, mining, and the gas and coal industries have directly or indirectly increased catastrophic methane (CH4) emissions at an alarming rate. Methane is 25 times more potent trapping heat when compared to carbon dioxide (CO2) in the atmosphere. A rise in atmospheric methane, on a 20-year time scale, has an impact of 80 times greater than that of CO2. With increased population growth, waste generation is rising and is predicted to reach 6 Mt by 2025. CH4 emitted from landfills is a significant source that accounts for 40% of overall global methane emissions. Various mitigation and emissions reduction strategies could significantly reduce the global CH4 burden at a cost comparable to the parallel and necessary CO2 reduction measures, reversing the CH4 burden to pathways that achieve the goals of the Paris Agreement. CH4 mitigation directly benefits climate change, has collateral impacts on the economy, human health, and agriculture, and considerably supports CO2 mitigation. Utilizing the CO2 from the environment, methanogens produce methane and lower their carbon footprint. NGOs and the general public should act on time to overcome atmospheric methane emissions by utilizing the raw source for producing carbon-neutral fuel. However, more research potential is required for green energy production and to consider investigating the untapped potential of methanogens for dependable energy generation.

Functional prediction of proteins from the human gut archaeome

The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.

Two-stage biohydrogen and methane production from sugarcane-based sugar and ethanol industrial wastes: A comprehensive review

The transition to renewable energy sources is crucial to ensure a sustainable future. Although the sugar and ethanol industries benefit from this transition, there are untapped opportunities to utilize the waste generated from the sugar and ethanol process chains through two-stage anaerobic digestion (TSAD). This review comprehensively discusses the utilization of various sugarcane-based industrial wastes by TSAD for sequential biohydrogen and methane production. Factors influencing TSAD process performance, including pH, temperature, hydraulic retention time, volatile fatty acids and alkalinity, nutrient imbalance, microbial population, and inhibitors, were discussed in detail. The potential of TSAD to reduce emissions of greenhouse gases is demonstrated. Recent findings, implications, and promising future research related to TSAD, including the integration of meta-omics approaches, gene manipulation and bioaugmentation, and application of artificial intelligence, are highlighted. The review can serve as important literature for the implementation, improvement, and advancements in TSAD research.

A robust genetic toolbox for fine-tuning gene expression in the CO2-Fixing methanogenic archaeon Methanococcus maripaludis

Libraries of well-characterized genetic elements for fine-tuning gene expression are essential for biological and biotechnological research and applications. The fast-growing and genetically tractable methanogen, Methanococcus maripaludis, is a promising host organism for biotechnological conversion of carbon dioxide and renewable hydrogen into fuels and value-added products, as well as fundamental biological studies of archaea. However, the lack of molecular tools for gene expression has hindered its application as a workhorse to fine-tune gene and metabolic pathway expressions. In this study, we developed a genetic toolbox, including libraries of promoters, ribosome binding sites (RBS), and neutral sites for chromosomal integration, to facilitate precise gene expression in M. maripaludis. We generated a promoter library consisting of 81 constitutive promoters with expression strengths spanning a ∼104-fold dynamic range. Importantly, we identified a base composition rule for strong archaeal promoters and successfully remodeled weak promoters, enhancing their activities by up to 120-fold. We also established an RBS library containing 42 diverse RBS sequences with translation strengths covering a ∼100-fold dynamic range. Additionally, we identified eight neutral sites and developed a one-step, Cas9-based marker-less knock-in approach for chromosomal integration. We successfully applied the characterized promoter and RBS elements to significantly improve recombinant protein expression by 41-fold and modulate essential gene expression to generate corresponding physiological changes in M. maripaludis. Therefore, this work establishes a solid foundation for utilizing this autotrophic methanogen as an ideal workhorse for archaeal biology and biotechnological studies and applications.

Eight Up-Coming Biotech Tools to Combat Climate Crisis

Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.

Magnetic biochar promotes the risk of mobile genetic elements propagation in sludge anaerobic digestion

Mobile genetic elements (MGEs) mediated horizontal gene transfer is the primary reason for the propagation of antibiotic resistance genes in environment. The behavior of MGEs under magnetic biochar pressure in sludge anaerobic digestion (AD) is still unknown. This study evaluated the effects of different dosage magnetic biochar on the MGEs in AD reactors. The results showed that the biogas yield was highest (106.68 ± 1.16 mL g^-1 VS_added) with adding optimal dosage of magnetic biochar (25 mg g^-1 TS_added), due to it increased the microorganism's abundance involved in hydrolysis and methanogenesis. While, the total absolute abundance of MGEs in the reactors with magnetic biochar addition increased by 11.58%-77.37% compared with the blank reactor. When the dosage of magnetic biochar was 12.5 mg g^-1 TS_added, the relative abundance of most MGEs was the highest. The enrichment effect on ISCR1 was the most significant, and the enrichment rate reached 158.90-214.16%. Only the intI1 abundance was reduced and the removal rates yield 14.38-40.00%, which was inversely proportional to the dosage of magnetic biochar. Co-occurrence network explored that Proteobacteria (35.64%), Firmicutes (19.80%) and Actinobacteriota (15.84%) were the main potential host of MGEs. Magnetic biochar changed MGEs abundance by affecting the potential MGEs-host community structure and abundance. Redundancy analysis and variation partitioning analysis showed that the combined effect of polysaccharides, protein and sCOD exhibited the greatest contribution (accounted for 34.08%) on MGEs variation. These findings demonstrated that magnetic biochar increases the risk of MGEs proliferation in AD system.

Insights into the impact of quaternary ammonium disinfectant on sewage sludge anaerobic digestion: Dose-response, performance variation, and potential mechanisms

Wide commercial applications of antimicrobial quaternary ammonium compounds (QACs) inevitably lead to the release into wastewater and enrichment in sewage sludge. This study evaluated the impacts of levels and structures of QACs on sewage sludge properties, microbial community, and methane production during anaerobic digestion. Methane production was stimulated or not affected at low QACs concentrations, but significantly inhibited at high QACs concentrations. Compared with benzyl and alkyltrimethyl QACs, dialkyl QACs showed least toxicity on digestion performance. Meanwhile, microbial community analysis indicated that shifts in bacterial communities mainly depended on QACs doses, but the archaeal communities were affected by both QACs doses and types. The dominant methanogenic pathway shifted from acetotrophic/methylotrophic methanogens to mixotrophic methanogens by low levels of benzyl and alkyltrimethyl QACs but not dialkyl QACs, and further to hydrogenotrophic methanogens at high QACs concentration. Mechanism exploration revealed that the presence of QACs promoted sludge solubilization by the integrated effects of cell lysis, electric neutralization, and hydrophobicity improvement, but inhibited methanogenesis due to the accumulation of volatile fatty acids and susceptibility of methanogens to QACs. These findings provided a reference for potential impacts of different QACs on sludge biological treatment, which had implications for the use and selection of QACs disinfectants.

Scale-up of biomass production by Methanococcus maripaludis

The development of a sustainable energy economy is one of the great challenges in the current times of climate crisis and growing energy demands. Industrial production of the fifth-generation biofuel methane by microorganisms has the potential to become a crucial biotechnological milestone of the post fossil fuel era. Therefore, reproducible cultivation and scale-up of methanogenic archaea (methanogens) is essential for enabling biomass generation for fundamental studies and for defining peak performance conditions for bioprocess development. This study provides a comprehensive revision of established and optimization of novel methods for the cultivation of the model organism Methanococcus maripaludis S0001. In closed batch mode, 0.05 L serum bottles cultures were gradually replaced by 0.4 L Schott bottle cultures for regular biomass generation, and the time for reaching peak optical density (OD₅₇₈) values was reduced in half. In 1.5 L reactor cultures, various agitation, harvesting and transfer methods were compared resulting in a specific growth rate of 0.16 h^-1 and the highest recorded OD₅₇₈ of 3.4. Finally, a 300-fold scale-up from serum bottles was achieved by growing M. maripaludis for the first time in a 22 L stainless steel bioreactor with 15 L working volume. Altogether, the experimental approaches described in this study contribute to establishing methanogens as essential organisms in large-scale biotechnology applications, a crucial stage of an urgently needed industrial evolution toward sustainable biosynthesis of energy and high value products.

CRISPR-Cas9 Toolkit for Genome Editing in an Autotrophic CO2-Fixing Methanogenic Archaeon

The CRISPR-Cas9 system is a robust genome editing tool that is widely applied in eukaryotes and bacteria. However, use of this technique has only been developed for one species of Archaea, a domain of life ranking in parallel with Eukarya and Bacteria. In this study, we applied the CRISPR-Cas9 genome editing technique to Methanococcus maripaludis, an autotrophic and hydrogenotrophic methanogenic archaeon with a remarkably polyploid genome comprising up to ~55 chromosomal copies per cell. An editing plasmid was designed that encodes small guide RNA (sgRNA), Cas9 protein and an ~1-kb repair template (donor). Highly efficient (75% to 100%) and precise genome editing was achieved following one-step transformation. Significantly, the Cas9-based system efficiently deleted one or two genes and a large DNA fragment (~9 kb) and even synchronously deleted 13 genes located at three loci in all chromosomal copies of M. maripaludis. Moreover, precise in situ genome modifications, such as gene tagging and multiple- and even single-nucleotide mutagenesis, were also introduced with high efficiency. Further, as a proof of concept, precise mutagenesis at the nucleotide level allowed the engineering of both transcriptional and translational activities. Mutations were introduced into an archaeal promoter BRE (transcription factor B [TFB] recognition element), a terminator U-tract region, and a gene coding region. Stop codon introduction into a gene through single-nucleotide substitution shut down its expression, providing an alternative strategy for gene inactivation. In conclusion, the robust CRISPR-Cas9 genetic toolkit developed in this investigation greatly facilitates the application of M. maripaludis as a model system in the study of archaeal biology and biotechnology development, particularly CO2-based biotechnologies. IMPORTANCE Archaea are prokaryotes with intriguing biological characteristics. They possess bacterial cell structures but eukaryotic homologous information processing machinery and eukaryotic featured proteins. Archaea also display excellent adaptability to extreme environments and play pivotal roles in ecological processes, thus exhibiting valuable biotechnological potential. However, the in-depth understanding and practical application of archaea are much lagging, because only a minority of pure cultures are available, and even worse, very few can be genetically manipulated. This work developed CRISPR-Cas9-based genome editing technology in Methanococcus maripaludis, a CO2-fixing methanogenic archaeon. The CRISPR-Cas9 approach developed in this study provides an elegant and efficient genome editing toolkit that can be applied in the knockout of single or multiple genes, in situ gene tagging, multiple- or single-nucleotide mutagenesis, and inactivation of gene expression by introduction of stop codons. The successful development of the CRISPR-Cas9 toolkit will facilitate the application of M. maripaludis in archaeal biology research and biotechnology development, particularly CO2-derived biotechnologies.

Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea

SignificanceBiological carbon fixation provides opportunities to directly utilize CO₂ to synthesize a broad range of value-added compounds, potentially displacing petroleum feedstock use in industry. Chemoautotrophs are particularly interesting as their carbon fixation can be driven chemically by renewable H₂ in place of light, which can limit industrial fermentation of photosynthetic organisms. We describe the development of a methanogenic host, Methanococcus maripaludis, for metabolic engineering. Since redox cofactors used in upstream archaeal carbon fixation pathways are orthogonal to typical downstream biosynthetic pathways, it was necessary to engineer both NADH biosynthesis and turnover. In doing so, we are able to show that methanogenic archaea can, indeed, serve as a platform for the high-yield production of bioplastics and monomers from CO₂ and H₂.

Cation exchange resin pretreatment enhancing methane production from anaerobic digestion of waste activated sludge

The application of anaerobic digestion (AD) to treat waste activated sludge (WAS) still exhibits some limitations, such as low methane production. In this study, cation exchange resin (CER) pretreatment was explored to enhance the efficiency of the AD of WAS. Based on the response surface methodology, the optimal conditions for CER pretreatment were reaction time of 7.4 h, 33.8 g CER (wet weight) /g volatile solids and sludge total solids of 2.4%. Under these optimal CER pretreatment conditions, approximately 30% of metals were removed from the WAS, particularly organic-binding metals. This metal removal disrupted the structures of extracellular polymer substances and led to sludge deflocculation, thereby releasing large amounts of organic substances from the sludge solids. Batch AD experiments showed that CER pretreatment increased the maximal production of volatile fatty acids and methane by 565.7% and 80.5%, respectively. Additionally, CER pretreatment promoted each stage of AD (i.e. solubilisation, hydrolysis, acidification and methanation) and the corresponding activities of key enzymes. Experimental results for semi-continuous AD further confirmed that CER pretreatment enhanced the proportion of methane in the biogas (from 62.75 ± 2.14% to 73.96 ± 0.99%) and the production of methane. An analysis of changes in the microbial communities demonstrated that CER pretreatment enhanced the abundance of microorganisms involved in hydrolysis, acidification and acetification and changed the major methanogenic pathway from acetoclastic methanogens to methylotrophic methanogens. These findings are expected to provide a reference for developing new pretreatment methods for enhancing anaerobic biodegradability of organic matters.

Effect of antibiotic mixtures on the characteristics of soluble microbial products and microbial communities in upflow anaerobic sludge blanket

Two upflow anaerobic sludge blanket reactors (UASBs) were used to investigate the effects of three antibiotic mixtures (erythromycin, sulfamethoxazole, and tetracycline) on reactor performance, soluble microbial products (SMPs) composition and microbial community. One reactor (UASB_antibiotics) was fed with antibiotic mixtures, whereas another reactor (UASB_control) was used as a control without the addition of antibiotic mixtures. Compared with those in UASB_control, UASB_antibiotics show lower chemical oxygen demand removal efficiency and biogas content. A higher removal efficiency of antibiotic mixtures was obtained in first few stages in UASB_antibiotics. The SMPs composition of effluent from the two reactors did not differ significantly, and the main components were protein-like substances, which produced higher fluorescence intensity in UASB_antibiotics. Gas chromatography-mass spectrometry analysis revealed that the main compounds identified as SMPs (<580 Da) were alkanes, aromatics and esters, with only 20% similarity of SMPs between UASB_antibiotics and UASB_control. Antibiotics had a significant effect on the microbial community structure. Notably, in UASB_control, hydrogenotrophic methanogens, key microorganisms in anaerobic digestion, had an obvious advantage at all stages compared with UASB_antibiotics, whereas acetoclastic methanogen exhibited the opposite pattern. The above results demonstrated that antibiotic mixtures influenced the effluent quality during anaerobic treatment of synthetic wastewater, resulting in changes in the microbial community structure. This study clarified the effect of antibiotic mixtures on the operation of UASBs. It could contribute to identifying potential strategies for improving effluent quality in anaerobic treatment.

Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis

Methanococcus maripaludis is a rapidly growing, hydrogenotrophic, and genetically tractable methanogen with unique capabilities to convert formate and CO₂ to CH₄. The existence of genome-scale metabolic models and an established, robust system for both large-scale and continuous cultivation make it amenable for industrial applications. However, the lack of molecular tools for differential gene expression has hindered its application as a microbial cell factory to produce biocatalysts and biochemicals. In this study, a library of differentially regulated promoters was designed and characterized based on the pst promoter, which responds to the inorganic phosphate concentration in the growth medium. Gene expression increases by 4- to 6-fold when the medium phosphate drops to growth-limiting concentrations. Hence, this regulated system decouples growth from heterologous gene expression without the need for adding an inducer. The minimal pst promoter is identified and contains a conserved AT-rich region, a factor B recognition element, and a TATA box for phosphate-dependent regulation. Rational changes to the factor B recognition element and start codon had no significant impact on expression; however, changes to the transcription start site and the 5' untranslated region resulted in the differential protein production with regulation remaining intact. Compared to a previous expression system based upon the histone promoter, this regulated expression system resulted in significant improvements in the expression of a key methanogenic enzyme complex, methyl-coenzyme M reductase, and the potentially toxic arginine methyltransferase MmpX.

Empower C1: Combination of Electrochemistry and Biology to Convert C1 Compounds

The idea to somehow combine electrical current and biological systems is not new. It was subject of research as well as of science fiction literature for decades. Nowadays, in times of limited resources and the need to capture greenhouse gases like CO₂, this combination gains increasing interest, since it might allow to use C1 compounds and highly oxidized compounds as substrate for microbial production by "activating" them with additional electrons. In this chapter, different possibilities to combine electrochemistry and biology to convert C1 compounds into useful products will be discussed. The chapter first shows electrochemical conversion of C1 compounds, allowing the use of the product as substrate for a subsequent biosynthesis in uncoupled systems, further leads to coupled systems of biology and electrochemical conversion, and finally reaches the discipline of bioelectrosynthesis, where electrical current and C1 compounds are directly converted by microorganisms or enzymes. This overview will give an idea about the potentials and challenges of combining electrochemistry and biology to convert C1 molecules.

Enhancing methanogenic fermentation of waste activated sludge via isoelectric-point pretreatment: Insights from interfacial thermodynamics, electron transfer and microbial community

The usefulness of waste activated sludge (WAS) as an energy source is limited by the poor generation efficiency of methane from WAS, which is mainly due to the complex nature of sludge and low abundance of functional microbes. In this study, the interfacial thermodynamics, electron transfer and microbial community of sludge were investigated to reveal the enhancing effects of isoelectric-point (pI) pretreatment on the efficiency of methane generation from WAS. Experimentally, after pI pretreatment, the methane production potential, maximum methane production rate and maximum methane proportion in the biogas increased by 122.2%, 154.4% and 17.4%, respectively, indicating that pI pretreatment enhanced the generation efficiency of methane. Analyses of changes in the solid-liquid interfacial non-covalent interaction energy, electron transfer capacity (ETC) and reductive peak potential values of sludge samples with and without pI pretreatment during a 170-day methanogenic fermentation period revealed that pI pretreatment enhanced the self-driven solid-liquid interfacial hydrophobic attractions of sludge, increased the abiotic driving forces of interfacial enzymatic reactions, promoted the electron transfer efficiency and lowered the barrier of the reduction reaction. It was thus hypothesised that these changes would be responsible for increasing methane production, which was confirmed by the correlation analyses between the interfacial free energy (IFE) and ETC versus daily methane production. Moreover, statistical analyses of the differences between the microbial communities of sludge samples with and without pI pretreatment during fermentation demonstrated that pI pretreatment significantly (P < 0.05) improved the relative abundances of the main functional microbes with respect to hydrolysis, acidification and methanation. A further investigation of the relationships of IFE and ETC with the relative abundances of the main genera of methanogens indicated that the hydrophobic attraction of sludge surface and a high ETC are conducive to the enrichment of hydrogenotrophic methanogens (+29.9%). These findings are expected to provide a conceptual framework for developing second-generation pretreatment methods and provide a methodological reference for revealing the details of the 'black-box' anaerobic digestion process.

Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories

Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH₄) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH₄ production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH₄ cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyr^α444 Gly^α445 Tyr^α446 in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH₄ production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.

Methyl-Coenzyme M Reductase and Its Post-translational Modifications

The methyl-coenzyme M reductase (MCR) is a central enzyme in anaerobic microbial methane metabolism, which consists of methanogenesis and anaerobic oxidation of methane (AOM). MCR catalyzes the final step of methanogenesis and the first step of AOM to achieve the production and oxidation of methane, respectively. Besides a unique nickel tetrahydrocorphinoid (coenzyme F430), MCR also features several unusual post-translational modifications (PTMs), which are assumed to play important roles in regulating MCR functions. However, only few studies have been implemented on MCR PTMs. Therefore, to recapitulate current knowledge and prospect future studies, this review summarizes and discusses studies on MCR and its PTMs.

Posttranslational Methylation of Arginine in Methyl Coenzyme M Reductase Has a Profound Impact on both Methanogenesis and Growth of Methanococcus maripaludis

Catalyzing the key step for anaerobic production and/or oxidation of methane and likely other short-chain alkanes, methyl coenzyme M reductase (Mcr) and its homologs play a key role in the global carbon cycle. The McrA subunit possesses up to five conserved posttranslational modifications (PTMs) at its active site. It was previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To systematically examine its physiological role, mmpX (locus tag MMP1554), the gene encoding Mmp10 in Methanococcus maripaludis, was deleted with a new genetic tool, resulting in the complete loss of the 5-C-(S)-methylarginine PTM of residue 275 in the McrA subunit. When the ΔmmpX mutant was complemented with the wild-type gene expressed by either a strong or a weak promoter, methylation was fully restored. Compared to the parental strain, maximal rates of methane formation by whole cells were reduced by 40 to 60% in the ΔmmpX mutant. The reduction in activity was fully reversed by the complement with the strong promoter. Site-directed mutagenesis of mmpX resulted in a differential loss of arginine methylation among the mutants in vivo, suggesting that activities of Mmp10 directly modulated methylation. R²⁷⁵ was present in a highly conserved PXRR²⁷⁵(A/S)R(G/A) signature sequence in McrAs. The only other protein in M. maripaludis containing a similar sequence was not methylated, suggesting that Mmp10 is specific for McrA. In conclusion, Mmp10 modulates the methyl-Arg PTM on McrA in a highly specific manner, which has a profound impact on Mcr activity.IMPORTANCE Mcr is the key enzyme in methanogenesis and a promising candidate for bioengineering the conversion of methane to liquid fuel. Our knowledge of Mcr is still limited. In terms of complexity, uniqueness, and environmental importance, Mcr is more comparable to photosynthetic reaction centers than conventional enzymes. PTMs have long been hypothesized to play key roles in modulating Mcr activity. Here, we directly link the mmpX gene to the arginine PTM of Mcr, demonstrate its association with methanogenesis activity, and offer insights into its substrate specificity and putative cofactor binding sites. This is also the first time that a PTM of McrA has been shown to have a substantial impact on both methanogenesis and growth in the absence of additional stressors.

Nature's recyclers: anaerobic microbial communities drive crude biomass deconstruction

Microbial communities within anaerobic ecosystems have evolved to degrade and recycle carbon throughout the earth. A number of strains have been isolated from anaerobic microbial communities, which are rich in carbohydrate active enzymes (CAZymes) to liberate fermentable sugars from crude plant biomass (lignocellulose). However, natural anaerobic communities host a wealth of microbial diversity that has yet to be harnessed for biotechnological applications to hydrolyze crude biomass into sugars and value-added products. This review highlights recent advances in 'omics' techniques to sequence anaerobic microbial genomes, decipher microbial membership, and characterize CAZyme diversity in anaerobic microbiomes. With a focus on the herbivore rumen, we further discuss methods to discover new CAZymes, including those found within multi-enzyme fungal cellulosomes. Emerging techniques to characterize the interwoven metabolism and spatial interactions between anaerobes are also reviewed, which will prove critical to developing a predictive understanding of anaerobic communities to guide in microbiome engineering.