Isolation of a methyl-reducing methanogen outside the Euryarchaeota

Anaerobic membrane distillation bioreactors for saline organic wastewater treatment: Impacts of salt accumulation on methanogenesis and microbial community

Anaerobic membrane distillation bioreactor (AnMDBR), which possesses several distinctive advantages such as high-quality water production, desalination and methanogenesis, shows enormous potential in saline organic wastewater (SAOW) treatment. However, salt accumulation in the reactor may deactivate anaerobic organisms and impede methanogenesis. In this work, effects of salt accumulation were comprehensively investigated regarding pollutant removal performance and methanogenesis in AnMDBRs over a 30-d operation. The investigative influent salinity was in the range of 0.0-2.0 %. The results demonstrated that AnMDBR achieved excellent chemical oxygen demand (COD) rejection (> 97 %) in the stabilization phase regardless of influent salinity. Moreover, the methane production was as high as 267 mL/gCOD, when the influent salinity did not exceed 1.0 %. When the influent salinity increased to 2.0 %, the methane production was significantly restricted, because salt stress altered the microbial community, resulting in a more sensitive and fragile ecosystem. Thermophilic and halophilic bacteria genera (Bacillus and Caproiciproducens) were selectively enriched in AnMDBR, promoting short-chain fatty acids generation. Meanwhile, these bacteria severely suppressed methanogenic archaea Methanosarcina, leading to an 80 % reduction in species abundance compared to a robust reactor. Furthermore, the salt stress inactivated key enzymes (mtr and mcr), disrupting methanogenic metabolism.

Decoding the Chemical Language of Ribosomally Synthesized and Post-Translationally Modified Peptides from the Untapped Archaea Domain

Chemical communication is crucial in ecosystems with complex microbial communities. However, the difficulties inherent to the cultivation of archaea have led to a limited understanding of their chemical language, especially regarding the structure diversity and function of secondary metabolites (SMs). Our in-depth exploration into the biosynthetic potential of archaea has unveiled the previously unexplored biosynthetic capabilities and chemical diversity of archaeal ribosomally synthesized and post-translationally modified peptides (RiPPs). Through the first application of heterologous expression in archaeal SM discovery, we have identified 24 lanthipeptides, including a distinctive type featuring diamino-dicarboxylic termini. It highlights the uniqueness of archaeal biosynthetic pathways and significantly expands the chemical landscape of archaeal SMs. Additionally, archaeal lanthipeptides demonstrate antagonistic activity against haloarchaea, mediating the unique biotic interaction in the halophilic niche. They showcase a new ecological role of RiPPs in enhancing the host's motility by inducing the rod-shaped cell morphology and upregulating the archaellin gene expression, facilitating the archaeal interaction with abiotic environments. These discoveries broaden our understanding of archaeal chemical language and provide promising prospects for future exploration of SM-mediated interaction.

Diversity and function of soluble heterodisulfide reductases in methane-metabolizing archaea

Soluble heterodisulfide reductase subunit A (HdrA) is an ancient protein central to energy metabolism, facilitating the recycling of intermediates in methane metabolism and performing flavin-based electron bifurcation for energy conservation. In this study, we investigated the functional diversity and evolutionary dynamics of HdrA in methane-metabolizing archaea. An analysis of 1,152 HdrA sequences from 624 genomes revealed that HdrA diversified through internal domain modifications, resulting in 28 distinct classes and 4 major types (types I, Ia, II, and III). Functional genes in HdrA gene clusters revealed variations in mid-potential electron donors, including NADH, F420H2, H2, and formate. Two major types of HdrA have not previously been studied in detail. Type II HdrA resulted from a fusion of two different classes of type I HdrA. Particularly, a consistent gene cluster containing type II HdrA, molybdopterin oxidoreductase, and F420 dehydrogenase was identified in anaerobic methane-oxidizing archaea and methanogens. Protein sequence and structural predictions suggested that the molybdopterin oxidoreductase protein had lost its catalytic function, and F420H2 served as the mid-potential electron donor or acceptor for the Hdr protein complex. This gene cluster may expand to include additional type I HdrA and HdrD, potentially supporting two electron bifurcation events to lower electron potential for ferredoxin reduction. Type III HdrA, with an inserted GltD domain compared to type I HdrA, appears to have altered the electron transfer route and may use NADH as its mid-potential electron donor or acceptor. The remarkable functional flexibility of HdrA likely helps methane-metabolizing archaea adapt to diverse anaerobic environments.IMPORTANCEAll methanogenic archaea use heterodisulfide of coenzymes M and B as the terminal electron acceptor. In anaerobic methane- and alkane-oxidizing archaea, the reverse reaction occurs. The cycling of heterodisulfide is vital to the energy conservation of these anaerobic microorganisms. Soluble heterodisulfide reductase is an ancient protein fulfilling this function via flavin-based electron bifurcation or confurcation. Despite being present in the vast majority of methane- and alkane-metabolizing archaea, the diversity and evolution of this key protein have not been investigated. This study reveals substantial domain variation and structural changes in the key bifurcating subunit HdrA in methane- and alkane-metabolizing archaea. The resulting flexibility of HdrA enables the protein complex to vary its interacting subunits and electron carriers based on the organisms' primary metabolism. Our findings shed light on how methane- and alkane-metabolizing archaea thrive in various anaerobic environments, contributing to our broader understanding of carbon cycling and energy conservation.

Gelling and reducing agents are potential carbon and energy sources in culturing of anaerobic microorganisms

The majority of microorganisms in the environment have yet to be isolated in pure cultures, and the reasons behind this phenomenon remain elusive. In this study, we investigated the possibility of the commonly used gelling agent including agar and gellan gum as a source of carbon and energy in anaerobic roll-tube cultivation from one mangrove sediment sample and two high-temperature oilfield samples. Based on growth tests and genomic evidence, anaerobic gellan degraders were retrieved from genera of Clostridium, Lacrimispora, and lineages from the rarely cultivated phylum Atribacterota. Anaerobic agarolytic microorganisms were found to be members of Bacillus and Clostridium. We also proved the role of carbon and energy sources of L-cysteine, a routine agent used to make culture media anoxic/anaerobic in both enrichment cultures and isolated strains representing Acetomicrobium, Thermodesulfovibrio, Lacrimispora, Clostridium, Bacillus, Coprothermobacter, Citrobacter, and Enterobacter. Furthermore, the isolates and enriched microbial communities utilizing L-cysteine under anaerobic conditions were mainly through L-cysteine desulfuration to pyruvate, ammonia, and sulfide. This study demonstrates that the widely used gelling and reducing agents in the basal medium can serve as carbon and energy sources for anaerobic microorganisms and thus may bias the enrichment and isolation.

IMPORTANCE

Most microbial species inhabiting natural environments have not been isolated in pure cultures using conventional media and laboratory conditions, but the reason behind this is unclear. Here, we provided a new explanation for the phenomenon, in that both the gelling agents, like agar and gellan gum, and reducing agent L-cysteine-HCl in the media provide extra carbon and energy sources to microorganisms and therefore decrease the chance in isolation specifically for the supplemented substrate which is supposed to be the sole source of carbon and energy. This result demonstrated that further improvement in the effectiveness of isolation of targeted microorganisms will be facilitated by subtracting the overlooked organic ingredients in the medium and more innovations.

Cometabolism of ferrihydrite reduction and methyl-dismutating methanogenesis by Methanosarcina mazei

Recent discoveries have shown that some Methanosarcina species can reduce Fe(III), reshaping our understanding of Methanosarcina ecophysiology. However, the specific minerals reduced, the products formed, and the underlying metabolic mechanisms remain elusive. Here, we report on the cometabolic process of Fe(III) reduction and methylotrophic methanogenesis in Methanosarcina mazei zm-15. Biogeochemical and mineralogical analyses were conducted to investigate Fe(III) reduction from three mineral preparations-ferrihydrite, goethite, and hematite. The results revealed that 38% of the 6 mM Fe(III) in ferrihydrite was reduced within 4 days, and this percentage increased to 75% with the addition of 100 µM anthraquinone-2,6-disulfonate (AQDS). Active Fe(III) reduction occurred immediately and preceded rapid methanogenesis. The addition of ferrihydrite and AQDS together significantly enhanced the maximal CH₄ production rate. However, Fe(III) reduction did not occur in goethite or hematite, even with the addition of 100 µM AQDS. Vivianite was identified as the major product from ferrihydrite reduction. Transcriptomic analysis revealed that gene expression related to the oxidation branch of the methyl-dismutating pathway and the membrane-associated electron transport chain (ETC) was significantly upregulated, whereas the expressions of genes associated with the reduction branch of the methyl-dismutating pathway were downregulated. In conclusion, M. mazei zm-15 demonstrates a strong ability to reduce poorly crystalline ferrihydrite, but not highly crystalline goethite and hematite. During the cometabolism of Fe(III) reduction and CH₄ production from methanol, the methyl-oxidation and membrane ETC pathways are enhanced, while the methyl-reduction pathway is downregulated. The mechanism of electron relay from cells to ferrihydrite, however, remains unclear and warrants further investigation.IMPORTANCEThe recent discovery that certain Methanosarcina species can grow by reducing Fe(III) challenges the traditional understanding of methanogens. However, the underlying metabolic mechanisms remain largely unexplored. Using a combination of biogeochemical, mineralogical, and microbiological approaches, we investigated the ability of Methanosarcina mazei zm-15. It exhibited a strong capacity to reduce poorly crystalline ferrihydrite but not highly crystalline goethite and hematite. The formation of vivianite from ferrihydrite reduction is likely due to the high rate of Fe(III) reduction and the presence of excess phosphorus in incubations. During the cometabolism of Fe(III) reduction and CH4 production from methanol, the methyl-oxidation and membrane electron transport pathways are upregulated, while the methyl-reduction pathway is downregulated. Our research uncovers a differential regulation of metabolic pathways during the cometabolism of Fe(III) reduction and CH4 production from methanol. The findings shed new light on the adaptive strategies employed by M. mazei in environments with the presence of Fe(III) and suggestthat Methanosarcina can play a significant role in methane production and iron cycling in natural environments.

Methane cycle in subsurface environment: A review of microbial processes

Methane is a pivotal component of the global carbon cycle. It acts both as a potent greenhouse gas and a vital energy source. While the microbial cycling of methane in subsurface environments is crucial, its impact on geological settings and related engineering projects is often underestimated. This review uniquely integrates the latest findings on methane production, oxidation, and migration processes in strata, revealing novel microbial mechanisms and their implications for environmental sustainability. We address critical issues of methane leakage and engineering safety during resource extraction, underscoring the urgent need for effective methane management strategies. This work clarifies geological factors affecting methane budgets and emissions, deepening our understanding of methane dynamics. It offers practical insights for geological engineering and sustainable natural gas hydrate exploration, paving the way for future research and applications.

Group-specific Quantification of mcrA genes of Methanogenic Archaea and "Candidatus Methanoperedens" by Digital PCR

Digital PCR is a technique that quantifies target genes based on the absence or presence of the targets in PCR amplicons. The present study exami-ned group-specific probes for the quantification of mcrA genes in six methanogenic archaeal groups and "Candidatus Methanoperedens" by digital PCR with the universal primers ML-f and ML-r. A digital PCR ana-lysis of paddy field soil detected all the targets, with the dominant and minor groups being Methanomicrobiales and Methanobrevibacter spp., respectively (107 and 104 copies [g dry soil]-1). This method has the potential to reveal the dynamics of specific methanogenic archaeal groups in the environment.

Unraveling methanogenesis processes and pathways for Quaternary shallow biogenic gas in aquifer systems through geochemical, genomic and transcriptomic analyses

Shallow biogenic gas is crucial in global warming and carbon cycling. Considering the knowledge gap in the understanding of methanogenesis and metabolic mechanisms within shallow groundwater systems, we investigated Quaternary shallow biogenic gas resources from the Hetao Basin in North China, which were previously underexplored. We systematically analyzed the genesis of gas and formation water, microbial communities, methanogenic processes, and pathways using geochemistry, genomics, and transcriptomics. Our findings indicated that active freshwater environments are conducive to microbial activity and the generation of primary microbial gases. A diverse range of microbes with functions, such as hydrolysis (e.g., Caulobacter), acidogenesis, and hydrogen production (e.g., Sediminibacterium), synergistically contributed to the methanogenic process. Methanogens predominantly comprised hydrogenotrophic methanogens (e.g., Methanobacteriales), although H2-dependent methylotrophic methanogens (e.g., Methanofastidiosa) were also prevalent. The metabolic processes of the different methanogenic pathways were revealed based on functional gene analysis and mapping results. Furthermore, the composition of the community structure, functional predictions, metagenomics, and metatranscriptomics underscored the contribution of the hydrogenotrophic pathway, which ranged from 52.22 % to 79.23 %. The aceticlastic pathway exhibited high gene abundance and was primarily associated with methylotrophs and other potential pathways. The H2-dependent methylotrophic methanogenesis pathway was constrained by low metabolic activity. By revealing the methane production mechanism of biogenic gas in shallow aquifer systems, this study provides a new perspective and profound comprehension of its ecological and environmental implications worldwide.

Nanopore sequencing: flourishing in its teenage years

Over the past decade, nanopore sequencing has experienced significant advancements and changes, transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing. However, as advancements in next-generation sequencing technology persist, nanopore sequencing also improves. This paper reviews the developments, applications, and outlook on nanopore sequencing technology. Currently, nanopore sequencing supports both DNA and RNA sequencing, making it widely applicable in areas such as telomere-to-telomere (T2T) genome assembly, direct RNA sequencing (DRS), and metagenomics. The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams, signaling a transformative influence on life science research. As the nanopore sequencing technology advances, it provides a faster, more cost-effective approach with extended read lengths, demonstrating the significant potential for complex genome assembly, pathogen detection, environmental monitoring, and human disease research, offering a fresh perspective in sequencing technologies.

Genome reduction in novel, obligately methyl-reducing Methanosarcinales isolated from arthropod guts (Methanolapillus gen. nov. and Methanimicrococcus)

Recent metagenomic studies have identified numerous lineages of hydrogen-dependent, obligately methyl-reducing methanogens. Yet, only a few representatives have been isolated in pure culture. Here, we describe six new species with this capability in the family Methanosarcinaceae (order Methanosarcinales), which makes up a substantial fraction of the methanogenic community in arthropod guts. Phylogenomic analysis placed the isolates from cockroach hindguts into the genus Methanimicrococcus (M. hacksteinii, M. hongohii, and M. stummii) and the isolates from millipede hindguts into a new genus, Methanolapillus (M. africanus, M. millepedarum, and M. ohkumae). Members of this intestinal clade, which includes also uncultured representatives from termites and vertebrates, have substantially smaller genomes (1.6-2.2 Mbp) than other Methanosarcinales. Genome reduction was accompanied by the loss of the upper part of the Wood-Ljungdahl pathway, several energy-converting membrane complexes (Fpo, Ech, and Rnf), and various biosynthetic pathways. However, genes involved in the protection against reactive oxygen species (catalase and superoxide reductase) were conserved in all genomes, including cytochrome bd (CydAB), a high-affinity terminal oxidase that may confer the capacity for microaerobic respiration. Since host-associated Methanosarcinales are nested within omnivorous lineages, we conclude that the specialization on methyl groups is an adaptation to the intestinal environment.

Cultivation and visualization of a methanogen of the phylum Thermoproteota

Methane is the second most abundant climate-active gas, and understanding its sources and sinks is an important endeavour in microbiology, biogeochemistry, and climate sciences1,2. For decades, it was thought that methanogenesis, the ability to conserve energy coupled to methane production, was taxonomically restricted to a metabolically specialized group of archaea, the Euryarchaeota1. The discovery of marker genes for anaerobic alkane cycling in metagenome-assembled genomes obtained from diverse habitats has led to the hypothesis that archaeal lineages outside the Euryarchaeota are also involved in methanogenesis3-6. Here we cultured Candidatus Methanosuratincola verstraetei strain LCB70, a member of the archaeal class Methanomethylicia (formerly Verstraetearchaeota) within the phylum Thermoproteota, from a terrestrial hot spring. Growth experiments combined with activity assays, stable isotope tracing, and genomic and transcriptomic analyses demonstrated that this thermophilic archaeon grows by means of methyl-reducing hydrogenotrophic methanogenesis. Cryo-electron tomography revealed that Ca. M. verstraetei are coccoid cells with archaella and chemoreceptor arrays, and that they can form intercellular bridges connecting two to three cells with continuous cytoplasm and S-layer. The wide environmental distribution of Ca. M. verstraetei suggests that they might play important and hitherto overlooked roles in carbon cycling within diverse anoxic habitats.