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

Methanothermobacter thermautotrophicus and Alternative Methanogens: Archaea-Based Production

Methanogenic archaea convert bacterial fermentation intermediates from the decomposition of organic material into methane. This process has relevance in the global carbon cycle and finds application in anthropogenic processes, such as wastewater treatment and anaerobic digestion. Furthermore, methanogenic archaea that utilize hydrogen and carbon dioxide as substrates are being employed as biocatalysts for the biomethanation step of power-to-gas technology. This technology converts hydrogen from water electrolysis and carbon dioxide into renewable natural gas (i.e., methane). The application of methanogenic archaea in bioproduction beyond methane has been demonstrated in only a few instances and is limited to mesophilic species for which genetic engineering tools are available. In this chapter, we discuss recent developments for those existing genetically tractable systems and the inclusion of novel genetic tools for thermophilic methanogenic species. We then give an overview of recombinant bioproduction with mesophilic methanogenic archaea and thermophilic non-methanogenic microbes. This is the basis for discussing putative products with thermophilic methanogenic archaea, specifically the species Methanothermobacter thermautotrophicus. We give estimates of potential conversion efficiencies for those putative products based on a genome-scale metabolic model for M. thermautotrophicus.

An improved CRISPR and CRISPR interference (CRISPRi) toolkit for engineering the model methanogenic archaeon Methanococcus maripaludis

BACKGROUND

The type II based CRISPR-Cas system remains restrictedly utilized in archaea, a featured domain of life that ranks parallelly with Bacteria and Eukaryotes. Methanococcus maripaludis, known for rapid growth and genetic tractability, serves as an exemplary model for studying archaeal biology and exploring CO2-based biotechnological applications. However, tools for controlled gene regulation remain deficient and CRISPR-Cas tools still need improved in this archaeon, limiting its application as an archaeal model cellular factory.

RESULTS

This study not only improved the CRISPR-Cas9 system for optimizing multiplex genome editing and CRISPR plasmid construction efficiencies but also pioneered an effective CRISPR interference (CRISPRi) system for controlled gene regulation in M. maripaludis. We developed two novel strategies for balanced expression of multiple sgRNAs, facilitating efficient multiplex genome editing. We also engineered a strain expressing Cas9 genomically, which simplified the CRISPR plasmid construction and facilitated more efficient genome modifications, including markerless and scarless gene knock-in. Importantly, we established a CRISPRi system using catalytic inactive dCas9, achieving up to 100-fold repression on target gene. Here, sgRNAs targeting near and downstream regions of the transcription start site and the 5'end ORF achieved the highest repression efficacy. Furthermore, we developed an inducible CRISPRi-dCas9 system based on TetR/tetO platform. This facilitated the inducible gene repression, especially for essential genes.

CONCLUSIONS

Therefore, these advancements not only expand the toolkit for genetic manipulation but also bridge methodological gaps for controlled gene regulation, especially for essential genes, in M. maripaludis. The robust toolkit developed here paves the way for applying M. maripaludis as a vital model archaeal cell factory, facilitating fundamental biological studies and applied biotechnology development of archaea.

Biohythane production via anaerobic digestion process: fundamentals, scale-up challenges, and techno-economic and environmental aspects

Biohythane, a balanced mixture comprising bioH2 (biohydrogen) and bioCH4 (biomethane) produced through anaerobic digestion, is gaining recognition as a promising energy source for the future. This article provides a comprehensive overview of biohythane production, covering production mechanisms, microbial diversity, and process parameters. It also explores different feedstock options, bioreactor designs, and scalability challenges, along with techno-economic and environmental assessments. Additionally, the article discusses the integration of biohythane into waste management systems and examines future prospects for enhancing production efficiency and applicability. This review serves as a valuable resource for researchers, engineers, and policymakers interested in advancing biohythane production as a sustainable and renewable energy solution.

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.

Mechanisms of microbial co-aggregation in mixed anaerobic cultures

Co-aggregation of anaerobic microorganisms into suspended microbial biofilms (aggregates) serves ecological and biotechnological functions. Tightly packed aggregates of metabolically interdependent bacteria and archaea play key roles in cycling of carbon and nitrogen. Additionally, in biotechnological applications, such as wastewater treatment, microbial aggregates provide a complete metabolic network to convert complex organic material. Currently, experimental data explaining the mechanisms behind microbial co-aggregation in anoxic environments is scarce and scattered across the literature. To what extent does this process resemble co-aggregation in aerobic environments? Does the limited availability of terminal electron acceptors drive mutualistic microbial relationships, contrary to the commensal relationships observed in oxygen-rich environments? And do co-aggregating bacteria and archaea, which depend on each other to harvest the bare minimum Gibbs energy from energy-poor substrates, use similar cellular mechanisms as those used by pathogenic bacteria that form biofilms? Here, we provide an overview of the current understanding of why and how mixed anaerobic microbial communities co-aggregate and discuss potential future scientific advancements that could improve the study of anaerobic suspended aggregates. KEY POINTS: • Metabolic dependency promotes aggregation of anaerobic bacteria and archaea • Flagella, pili, and adhesins play a role in the formation of anaerobic aggregates • Cyclic di-GMP/AMP signaling may trigger the polysaccharides production in anaerobes.

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

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.

Internal transcription termination widely regulates differential expression of operon-organized genes including ribosomal protein and RNA polymerase genes in an archaeon

Genes organized within operons in prokaryotes benefit from coordinated expression. However, within many operons, genes are expressed at different levels, and the mechanisms for this remain obscure. By integrating PacBio-seq, dRNA-seq, Term-seq and Illumina-seq data of a representative archaeon Methanococcus maripaludis, internal transcription termination sites (ioTTSs) were identified within 38% of operons. Higher transcript and protein abundances were found for genes upstream than downstream of ioTTSs. For representative operons, these differences were confirmed by northern blotting, qRT-PCR and western blotting, demonstrating that these ioTTS terminations were functional. Of special interest, mutation of ioTTSs in ribosomal protein (RP)-RNA polymerase (RNAP) operons not only elevated expression of the downstream RNAP genes but also decreased production of the assembled RNAP complex, slowed whole cell transcription and translation, and inhibited growth. Overexpression of the RNAP subunits with a shuttle vector generated the similar physiological effects. Therefore, ioTTS termination is a general and physiologically significant regulatory mechanism of the operon gene expression. Because the RP-RNAP operons are found to be widely distributed in archaeal species, this regulatory mechanism could be commonly employed in archaea.

Model Organisms To Study Methanogenesis, a Uniquely Archaeal Metabolism

Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments such as aquatic sediments, anaerobic digesters, inundated agricultural fields, the rumen of cattle, and the hindgut of termites, where they catalyze the terminal reactions in the degradation of organic matter. Methanogenesis is the only metabolism that is restricted to members of the domain Archaea. Here, we discuss the importance of model organisms in the history of methanogen research, including their role in the discovery of the archaea and in the biochemical and genetic characterization of methanogenesis. We also discuss outstanding questions in the field and newly emerging model systems that will expand our understanding of this uniquely archaeal metabolism.

Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis

Ribosomal RNA (rRNA) processing and maturation are fundamentally important for ribosome biogenesis, but the mechanisms in archaea, the third form of life, remains largely elusive. This study aimed to investigate the rRNA maturation process in Methanococcus maripaludis, a representative archaeon lacking known 3'-5' exonucleases. Through cleavage site identification and enzymatic assays, the splicing endonuclease EndA was determined to process the bulge-helix-bulge (BHB) motifs in 16S and 23S rRNA precursors. After splicing, the circular processing intermediates were formed and this was confirmed by quantitative RT-PCR and Northern blot. Ribonuclease assay revealed a specific cleavage at a 10-nt A/U-rich motif at the mature 5' end of pre-16S rRNA, which linearized circular pre-16S rRNA intermediate. Further 3'-RACE and ribonuclease assays determined that the endonuclease Nob1 cleaved the 3' extension of pre-16S rRNA, and so generated the mature 3' end. Circularized RT-PCR (cRT-PCR) and 5'-RACE identified two cleavage sites near helix 1 at the 5' end of 23S rRNA, indicating that an RNA structure-based endonucleolytic processing linearized the circular pre-23S rRNA intermediate. In the maturation of pre-5S rRNA, multiple endonucleolytic processing sites were determined at the 10-nt A/U-rich motif in the leader and trailer sequence. This study demonstrates that endonucleolytic processing, particularly at the 10-nt A/U-rich motifs play an essential role in the pre-rRNA maturation of M. maripaludis, indicating diverse pathways of rRNA maturation in archaeal species.

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.