Domain Archaea Research Articles

Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits

The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed efficiency states, even when fed an identical diet. Here, we reveal that many microbial populations belonging to the bacteria and archaea domains show divergent proteome production in function of the feed efficiency state. Thus, proteomic data serve as a strong indicator of host feed efficiency state phenotype, overpowering predictions based on genomic and taxonomic information. We highlight protein production of specific phylogenies associated with each of the feed efficiency states. We also find remarkable plasticity of the proteome both in the individual population and at the community level, driven by niche partitioning and competition. These mechanisms result in protein production patterns that exhibit functional redundancy and checkerboard distribution that are tightly linked to the host feed efficiency phenotype. By linking microbial protein production and the ecological mechanisms that act within the microbiome feed efficiency states, our present work reveals a layer of complexity that bears immense importance to the current global challenges of food security and sustainability.

Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes

Mining is among the human activities with widest environmental impacts, and mining-impacted environments are characterized by high levels of metals that can co-select for antibiotic resistance genes (ARGs) in microorganisms. However, ARGs in mining-impacted environments are still poorly understood. Here, we conducted a comprehensive study of ARGs in such environments worldwide, taking advantage of 272 metagenomes generated from a global-scale data collection and two national sampling efforts in China. The average total abundance of the ARGs in globally distributed studied mine sites was 1572 times per gigabase, being rivaling that of urban sewage but much higher than that of freshwater sediments. Multidrug resistance genes accounted for 40% of the total ARG abundance, tended to co-occur with multimetal resistance genes, and were highly mobile (e.g. on average 16% occurring on plasmids). Among the 1848 high-quality metagenome-assembled genomes (MAGs), 85% carried at least one multidrug resistance gene plus one multimetal resistance gene. These high-quality ARG-carrying MAGs considerably expanded the phylogenetic diversity of ARG hosts, providing the first representatives of ARG-carrying MAGs for the Archaea domain and three bacterial phyla. Moreover, 54 high-quality ARG-carrying MAGs were identified as potential pathogens. Our findings suggest that mining-impacted environments worldwide are underexplored hotspots of multidrug resistance genes.

Trans-kingdom interactions in mixed biofilm communities.

The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life, which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonize a surface develop architecturally complex surface-adhered communities, which we refer to as biofilms. They are embedded in polymeric structural scaffolds and serve as a dynamic milieu for intercellularcommunication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed coexistence of microorganisms from all domains of life, including Bacteria, Archaea, and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.

Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs.

Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.

High-Quality Complete Genome Resource of Pectobacterium parvum Isolate FN20211 CausingAerial Stem Rot of Potato.

High-Quality Complete Genome Resource of Pectobacterium parvum Isolate FN20211 CausingAerial Stem Rot of Potato.

Metagenomic-Metabolomic Mining of Kinema, a Naturally Fermented Soybean Food of the Eastern Himalayas.

Kinema is a popular sticky fermented soybean food of the Eastern Himalayan regions of North East India, east Nepal, and south Bhutan. We hypothesized that some dominant bacteria in kinema may contribute to the formation of targeted and non-targeted metabolites for health benefits; hence, we studied the microbiome–metabolite mining of kinema. A total of 1,394,094,912 bp with an average of 464,698,304 ± 120,720,392 bp was generated from kinema metagenome, which resulted in the identification of 47 phyla, 331 families, 709 genera, and 1,560 species. Bacteria (97.78%) were the most abundant domain with the remaining domains of viruses, eukaryote, and archaea. Firmicutes (93.36%) was the most abundant phylum with 280 species of Bacillus, among which Bacillus subtilis was the most dominant species in kinema followed by B. glycinifermentans, B. cereus, B. licheniformis, B. thermoamylovorans, B. coagulans, B. circulans, B. paralicheniformis, and Brevibacillus borstelensis. Predictive metabolic pathways revealed the abundance of genes associated with metabolism (60.66%), resulting in 216 sub-pathways. A total of 361 metabolites were identified by metabolomic analysis (liquid chromatography-mass spectrophotometry, LC-MS). The presence of metabolites, such as chrysin, swainsonine, and 3-hydroxy-L-kynurenine (anticancer activity) and benzimidazole (antimicrobial, anticancer, and anti-HIV activities), and compounds with immunomodulatory effects in kinema supports its therapeutic potential. The correlation between the abundant species of Bacillus and primary and secondary metabolites was constructed with a bivariate result. This study proves that Bacillus spp. contribute to the formation of many targeted and untargeted metabolites in kinema for health-promoting benefits.

DNA Metabarcoding Reveals Cryptic Diversity in Forest Soils on the Isolated Brazilian Trindade Island, South Atlantic.

Located 1140km from the South American coastline in the South Atlantic Ocean and with an age of 4 million years, Trindade Island is the most recent volcanic component of Brazilian territory. Its original native vegetation has been severely damaged by human influence, in particular through the introduction of exotic grazing animals such as goats. However, since the complete eradication of goats and other feral animals in the late 1990s, the island's vegetation has been recovering, and even some endemic species that had been considered extinct have been rediscovered. In this study, we set out to characterize the contemporary cryptic diversity in soils of the recovering native forest of Trindade Island using metabarcoding by high throughput sequencing (HTS). The sequence diversity obtained was dominated by microorganisms, including three domains (Bacteria, Archaea, and Eukarya) and five kingdoms (Fungi, Metazoa, Protozoa, Chromista, and Viridiplantae). Bacteria were represented by 20 phyla and 116 taxa, with Archaea by only one taxon. Fungi were represented by seven phyla and 250 taxa, Viridiplantae by five phyla and six taxa, Protozoa by five phyla and six taxa, Metazoa by three phyla and four taxa and Chromista by two phyla and two taxa. Even after the considerable anthropogenic impacts and devastation of the island's natural forest, our sequence data reveal the presence of a rich and complex diversity of microorganisms, invertebrates, and plants and provide important baseline biodiversity information that will contribute to ecological restoration efforts on the island.

Microbial and functional characterization of granulated sludge from full-scale UASB thermophilic reactor applied to sugarcane vinasse treatment

ABSTRACT Considering the scarcity of data in the literature regarding phylogenetic and metabolic composition of different inocula, especially those from thermophilic conditions, this research aimed at characterizing the microbial community and preferable metabolic pathways of an UASB reactor sludge applied to the thermophilic treatment (55°C) of sugarcane vinasse, by means of shotgun metagenomics. After its metabolic potential was depicted, it was possible to observe several genes encoding enzymes that are of great importance to anaerobic digestion processes with different wastes as substrate, especially regarding the biodegradation of carbohydrates and ligninolytic compounds, glycerolypids, volatile fatty acids and alcohols metabolism and biogas (H2 and CH4) production. The genera identified in higher relative abundances for Bacteria domain were Sulfirimonas (37.52 ± 1.8%), possibly related to the sludge endogenic activity due to its strong relation with a peptidoglycan lyase enzymes family, followed by Fluviicola (5.01 ± 1.0%), Defluviitoga (4.36 ± 0.2%), Coprothermobacter (4.32 ± 0.5%), Fervidobacterium (2.93 ± 0.3%), Marinospirillum (2.75 ± 0.2%), Pseudomonas (2.14 ± 0.2%) and Flavobacterium (1.78 ± 0.1%), mostly related with carbohydrates fermentations and/or H2 production. For Archaea domain, Methanosarcina (0.61 ± 0.1%), Methanothermobacter (0.38 ± 0.0%), Methanoculleus (0.30 ± 0.1%), Thermococcus (0.03 ± 0.0%), Methanolobus (0.02 ± 1.8%), Methanobacterium (0.013 ± 0.0%), Aciduliprofundum and Pyrococcus (0.01 ± 0.0%) were the most dominant ones, being Methanosarcina the most related with methanogenesis. It was concluded that the robust inoculum description performed in this study may subside future biotechnological researches by using similar inocula (UASB sludges), focusing on the obtainment of value-added by-products by means of anaerobic digestion, such as volatile fatty acids, alcohols and biogas (H2 and CH4), by using several types of waste as substrate.

Effect of Fe3O4 nanoparticles on microbial diversity and biogas production in anaerobic digestion of crude glycerol

This study investigated the effects of citrate-coated Fe3O4 nanoparticles in the anaerobic digestion of crude glycerol, the main by-product of the biodiesel industry. Fe3O4 nanoparticles were synthesized by the coprecipitation method and Scanning Electron Microscopy (SEM) characterized it. The method designed for synthesis produced stable Fe3O4 nanoparticles with diameters about 20 nm. Duplicate of anaerobic batch reactors (500 mL) were used for assessing the influence of Fe3O4 nanoparticles in four assays performed at 37 °C. The reactors were filled with anaerobic granular sludge; crude glycerol (25.0 g COD L−1); buffer solution; citrate-coated Fe3O4 nanoparticles suspension (0.2 g L−1; 0.4 g L−1 and; 0.8 g L−1 and a control without Fe3O4 nanoparticles); deionized water up to 250 mL. There were increases of 49.8%, 28.5% and 26.0% in the accumulated production of CH4 and 25.7%, 17.1% and 20.0% in the maximum rate of CH4 production in assays supplemented with 0.2, 0.4 and 0.8 g L−1 of Fe3O4 nanoparticles, respectively, in relation to control reactors. It was also observed a substantial increase on relative abundance of Bacteria and Archaea Domains, specially Bacteroides, Clostridiales, Methanomicrobiales and Methanosarcinales orders, after anaerobic digestion supplemented with Fe3O4 nanoparticles. The addition of Fe3O4 nanoparticles could improve the anaerobic digestion of crude glycerol, optimizing bacterial and archaeal communities enhancing the CH4 production.

Functional and Conformational Plasticity of an Animal Group 1 LEA Protein.

Group 1 (Dur-19, PF00477, LEA_5) Late Embryogenesis Abundant (LEA) proteins are present in organisms from all three domains of life, Archaea, Bacteria, and Eukarya. Surprisingly, Artemia is the only genus known to include animals that express group 1 LEA proteins in their desiccation-tolerant life-history stages. Bioinformatics analysis of circular dichroism data indicates that the group 1 LEA protein AfLEA1 is surprisingly ordered in the hydrated state and undergoes during desiccation one of the most pronounced disorder-to-order transitions described for LEA proteins from A. franciscana. The secondary structure in the hydrated state is dominated by random coils (42%) and β-sheets (35%) but converts to predominately α-helices (85%) when desiccated. Interestingly, AfLEA1 interacts with other proteins and nucleic acids, and RNA promotes liquid–liquid phase separation (LLPS) of the protein from the solvent during dehydration in vitro. Furthermore, AfLEA1 protects the enzyme lactate dehydrogenase (LDH) during desiccation but does not aid in restoring LDH activity after desiccation-induced inactivation. Ectopically expressed in D. melanogaster Kc167 cells, AfLEA1 localizes predominantly to the cytosol and increases the cytosolic viscosity during desiccation compared to untransfected control cells. Furthermore, the protein formed small biomolecular condensates in the cytoplasm of about 38% of Kc167 cells. These findings provide additional evidence for the hypothesis that the formation of biomolecular condensates to promote water stress tolerance during anhydrobiosis may be a shared feature across several groups of LEA proteins that display LLPS behaviors.

Methane formation driven by reactive oxygen species across all living organisms.

Methane (CH4), the most abundant hydrocarbon in the atmosphere, originates largely from biogenic sources1 linked to an increasing number of organisms occurring in oxic and anoxic environments. Traditionally, biogenic CH4 has been regarded as the final product of anoxic decomposition of organic matter by methanogenic archaea. However, plants2,3, fungi4, algae5 and cyanobacteria6 can produce CH4 in the presence of oxygen. Although methanogens are known to produce CH4 enzymatically during anaerobic energy metabolism7, the requirements and pathways for CH4 production by non-methanogenic cells are poorly understood. Here, we demonstrate that CH4 formation by Bacillus subtilis and Escherichia coli is triggered by free iron and reactive oxygen species (ROS), which are generated by metabolic activity and enhanced by oxidative stress. ROS-induced methyl radicals, which are derived from organic compounds containing sulfur- or nitrogen-bonded methyl groups, are key intermediates that ultimately lead to CH4 production. We further show CH4 production by many other model organisms from the Bacteria, Archaea and Eukarya domains, including in several human cell lines. All these organisms respond to inducers of oxidative stress by enhanced CH4 formation. Our results imply that all living cells probably possess a common mechanism of CH4 formation that is based on interactions among ROS, iron and methyl donors, opening new perspectives for understanding biochemical CH4 formation and cycling.

Metagenomic Analysis of the Long-Term Synergistic Effects of Antibiotics on the Anaerobic Digestion of Cattle Manure

The conversion of cattle manure into biogas in anaerobic digestion (AD) processes has been gaining attention in recent years. However, antibiotic consumption continues to increase worldwide, which is why antimicrobial concentrations can be expected to rise in cattle manure and in digestate. This study examined the long-term synergistic effects of antimicrobials on the anaerobic digestion of cattle manure. The prevalence of antibiotic resistance genes (ARGs) and changes in microbial biodiversity under exposure to the tested drugs was investigated using a metagenomic approach. Methane production was analyzed in lab-scale anaerobic bioreactors. Bacteroidetes, Firmicutes, and Actinobacteria were the most abundant bacteria in the samples. The domain Archaea was represented mainly by methanogenic genera Methanothrix and Methanosarcina and the order Methanomassiliicoccales. Exposure to antibiotics inhibited the growth and development of methanogenic microorganisms in the substrate. Antibiotics also influenced the abundance and prevalence of ARGs in samples. Seventeen types of ARGs were identified and classified. Genes encoding resistance to tetracyclines, macrolide–lincosamide–streptogramin antibiotics, and aminoglycosides, as well as multi-drug resistance genes, were most abundant. Antibiotics affected homoacetogenic bacteria and methanogens, and decreased the production of CH4. However, the antibiotic-induced decrease in CH4 production was minimized in the presence of highly drug-resistant microorganisms in AD bioreactors.

Microbial fuel cell coupled Fenton oxidation for the cathodic degradation of emerging contaminants from wastewater: Applications and challenges.

Urbanization and industrialization have resulted in the escalation of the occurrence of emerging contaminants (EC) in the wastewater and ultimately to the receiving water bodies due to their bio-refractory nature. The presence of ECs in the water bodies adversely affects all three domains of life, viz. bacteria, archaea and eukaryotes, and eventually the ecosystem. Fenton oxidation is one of the most suitable method that is capable of degrading a variety of ECs by employing a strong oxidizing agent in the form of •OH. The coupling of Fenton oxidation with microbial fuel cell (MFC) offers benefits, such as low-cost, minimal requirement of external energy, and in-situ generation of oxidizing agents. The resulting system, termed as bio-electro-Fenton MFC (BEF-MFC), is capable of degrading the ECs in the cathodic chamber, while harvesting bioelectricity and simultaneously removing oxidizable organic matter from wastewater in the anodic chamber. This review discusses the applications of BEF-MFC for the treatment of dyes, pharmaceuticals, pesticides, and real complex wastewaters. Additionally, the effect of operating conditions on the performance of BEF-MFC are elaborated and emphasis is also given on possible future direction of research that can be adopted in BEF-MFC in the purview of up-scaling.

Halorubrum pleomorphic virus-6 Membrane Fusion Is Triggered by an S-Layer Component of Its Haloarchaeal Host.

(1) Background: Haloarchaea comprise extremely halophilic organisms of the Archaea domain. They are single-cell organisms with distinctive membrane lipids and a protein-based cell wall or surface layer (S-layer) formed by a glycoprotein array. Pleolipoviruses, which infect haloarchaeal cells, have an envelope analogous to eukaryotic enveloped viruses. One such member, Halorubrum pleomorphic virus 6 (HRPV-6), has been shown to enter host cells through virus-cell membrane fusion. The HRPV-6 fusion activity was attributed to its VP4-like spike protein, but the physiological trigger required to induce membrane fusion remains yet unknown. (2) Methods: We used SDS-PAGE mass spectroscopy to characterize the S-layer extract, established a proteoliposome system, and used R18-fluorescence dequenching to measure membrane fusion. (3) Results: We show that the S-layer extraction by Mg2+ chelating from the HRPV-6 host, Halorubrum sp. SS7-4, abrogates HRPV-6 membrane fusion. When we in turn reconstituted the S-layer extract from Hrr. sp. SS7-4 onto liposomes in the presence of Mg2+, HRPV-6 membrane fusion with the proteoliposomes could be readily observed. This was not the case with liposomes alone or with proteoliposomes carrying the S-layer extract from other haloarchaea, such as Haloferax volcanii. (4) Conclusions: The S-layer extract from the host, Hrr. sp. SS7-4, corresponds to the physiological fusion trigger of HRPV-6.

Haloarchaea as emerging big players in future polyhydroxyalkanoate bioproduction: Review of trends and perspectives

Haloarchaea comprise the extremely halophilic branch of the phylum Euryarchaeota and they are members of the prokaryotic domain Archaea. They thrive best in extremely saline habitats with salt concentrations of 2 to 5 mol L–1 NaCl, and thus under conditions of near salt saturation in water. These ancient organisms are among the oldest species on Earth, and are characterized by ether-linked lipids in the cytoplasmic membrane and murein-free cell walls. Haloarchaea are increasingly receiving attention as microbial cell factories for the bioproduction of diverse marketable products, such as bacterioruberin, bacteriorhodopsin, isoprenoids, and polyhydroxyalkanoates (PHAs). These biopolyesters serve as intracellular storage compounds for secondary metabolism by haloarchaea and many other prokaryotes. Engineered or wild type PHA-producing haloarchaea that utilize inexpensive raw materials for bioproduction, and which only require clean-in-place procedures to run PHA production bioprocesses, are currently undergoing scale-up within the research and development field of Archaea Biotechnology. In addition, PHAs exhibit high potential as both bio-based and biodegradable plastic-like bulk products on the industrial biotechnology market (“White Biotechnology”) for biopolymers. However, PHA production by haloarchaea has not yet reached industrial maturity. The present review discusses the background, previous research, and biological role of PHA biosynthesis in haloarchaea, as well as current trends, and a critical discussion of its potential for broad industrialization.

Quantitative Mass Spectrometry by SILAC in Haloferax volcanii.

The development of mass spectrometry (MS)-based proteomics methods has been critical in providing new insight about cellular processes and adaptations in all domains of life. While traditional MS-based methods are not inherently quantitative, technologies are now available to overcome this limitation. Of note, stable isotope labeling of amino acids in cell culture (SILAC) is reported as a reliable tool to label proteomes for quantitative MS-based proteomics that is accurate and flexible for multiplexing. The isotopically labeled lysine and arginine are easily incorporated into the proteome of cells auxotrophic for these amino acids. Microorganisms of the domain Archaea provide a fascinating alternative to understanding cellular adaptations and responses to environmental stresses. However, the availability of preferred SILAC-based quantitative analyses is limited. This protocol describes the use of SILAC to quantitatively analyze the proteome of Haloferax volcanii, a mesophilic halophilic archaeon that is easy to grow and requires no special equipment to maintain.

Testing novel multicomposite materials for electromethanogenesis

Electromethanogenesis is an innovative technology that uses a microbial electrochemical system to produce methane from CO2, in a power-to-gas (BEP2G) concept. The results of experimental tests of new and cost-effective carbonaceous materials for electrode are presented here. The study aims at optimizing electromethanogenesis processes at laboratory level in mesothermic condition. As part of the experiments, hydrogenotrophic microorganisms (Family Metanobacteriaceae of Archaea domains) were selected from a mixed consortium taken from a biogas digestate and inoculated in double-chamber bioelectrochemical systems. The maximum amount of methane produced was 0.3 - 0.8 mol/m2g (normalized to the cathode area) with carbon cloth electrodes. Aiming at improving the methane productivity, innovative materials for the electrodes were now studied, creating porous high-surface composites, and studying nitrogen carbons doped with Cu and hydroxyapatite (Multicomposite Cu@/HAP/C), as chemical catalysts for CO2 reduction (CO2RR). The description of the procedure for the Multicomposite Cu@/HAP/C production is reported in detail.

Metal nanoparticles Biosynthesis Using the Halophilic Archaeon Haloferax volcanii.

Nanoparticle (NP) synthesis using biological resources as reducing agents is an eco-friendly and simple strategy compared to the traditional physical/chemical methods. The ability of microorganisms of the Archaea domain to synthesize metal NPs has been explored to a limited extent. Metal NPs have been applied in several fields including catalysis, agriculture, biomedicine, electronics, and optics. Recently we reported that the halophilic archaeon Haloferax volcanii is capable of synthesizing silver and gold NPs. In this work, we present a simple protocol for the obtention of metal NPs using this microorganism which may be also used as a starting point for assaying NP biosynthesis in other haloarchaea.

The Azurin Coding Gene: Origin and Phylogenetic Distribution.

Azurin is a bacterial-derived cupredoxin, which is mainly involved in electron transport reactions. Interest in azurin protein has risen in recent years due to its anticancer activity and its possible applications in anticancer therapies. Nevertheless, the attention of the scientific community only focused on the azurin protein found in Pseudomonas aeruginosa (Proteobacteria, Gammaproteobacteria). In this work, we performed the first comprehensive screening of all the bacterial genomes available in online repositories to assess azurin distribution in the three domains of life. The Azurin coding gene was not detected in the domains Archaea and Eucarya, whereas it was detected in phyla other than Proteobacteria, such as Bacteroidetes, Verrucomicrobia and Chloroflexi, and a phylogenetic analysis of the retrieved sequences was performed. Observed patchy distribution and phylogenetic data suggest that once it appeared in the bacterial domain, the azurin coding gene was lost in several bacterial phyla and/or anciently horizontally transferred between different phyla, even though a vertical inheritance appeared to be the major force driving the transmission of this gene. Interestingly, a shared conserved domain has been found among azurin members of all the investigated phyla. This domain is already known in P. aeruginosa as p28 domain and its importance for azurin anticancer activity has been widely explored. These findings may open a new and intriguing perspective in deciphering the azurin anticancer mechanisms and to develop new tools for treating cancer diseases.

Archaeal Communities of Frozen Quaternary Sediments of Marine Origin on the Coast of Western Spitsbergen

The archaeal composition of permafrost samples taken during the drilling of frozen marine sediments in the area of the Barentsburg coal mine on the east coast of Grønfjord Bay of Western Spitsbergen has been studied. This study is based on an analysis of the V4 region of the 16S rRNA gene, carried out using next-generation sequencing. The general phyla of the Archaea domain are Euryarchaeota, Bathyarchaeota, Thaumarchaeota, and Asgardarchaea. As a result of a phylogenetic analysis of the dominant operational taxonomic units, representatives of methanogenic and methane- and ammonium-oxidizing archaea, as well as heterotrophic archaea, are found. The methanogenic archaea of Euryarchaeota phylum, Methanobacteria class, are found in permafrost with controversial genesis, while the methane-oxidizing archaea of Methanomicrobia class Methanosarcinales order are found in the marine permafrost at cape Finneset: the ANME-2a, -2b group in layers of 8.6 and 11.7 m and the ANME-2d group (Candidatus Methanoperedens) in a layer of 6.5 m. Ammonium-oxidizing archaea of phylum Thaumarchaeota is present in all types of permafrost, while the order of Nitrososphaerales is found in permafrost with controversial genesis and the order Nitrosopumilales is in permafrost with marine and controversial genesis. Representatives of phylum Bathyarchaeota are found stratigraphically in the most ancient samples under study. Asgardarchaeota superfylum is excluded in the layers of permafrost with marine genesis and is represented by the phyla Lokiarchaeota, Thorarchaeota, and an unclassified group belonging to this superphylum. The presence of methane, ethylene, and ethane in the permafrost of the first sea terrace of Cape Finnemet at a depth of 11.7 m, as well as the composition of the archaeal community, give us reason to assume that, before freezing, microbiological processes of anaerobic methane oxidation took place in it, probably received from Tertiary rocks. The results of both this and previous works present the Spitsberen permafrost as a rich archive of genetic information of little-studied prokaryotic groups.