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Archaea synthesize heterochiral phospholipid membranes as revealed by chiral analysis of archaeols.

This study comprehensively characterizes structural diversity of archaeol lipids in selected archaeal genera, integrating available genomic information with advanced lipidomic and stereochemical analyzes. Study of genomes from six archaeal genera revealed the presence of key enzymes involved in glycerophosphate biosynthesis, namely glycerol-1-phosphate dehydrogenase and glycerol-3-phosphate dehydrogenase. Their coexistence in some of the studied strains suggests the ability of these organisms to synthesize both enantiomeric forms of glycerol phosphates. Shotgun lipidomic profiling confirmed th…

ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0.

DNA-binding transcription factors (TFs) have a central role in regulation of gene expression at the transcription initiation level. These proteins have been experimentally described in multiple bacterial and archaeal genomes. These descriptions have allowed their prediction in complete genomes. In this work, we collected 1784 experimentally validated TFs across 25 bacterial and seven archaeal phyla, including Gammaproteobacteria, Bacillota, and Actinomycetota in bacteria and Thermoproteota and Thermococci in archaea. The collection of regulatory proteins was organized into a relational databas…

Mercury methylation in methanogenic archaea: A protocol for stabilized cultivation and accurate assessment.

Although methanogenic archaea are among the oldest microorganisms capable of mercury methylation, their contribution to methylmercury (MeHg) production has only recently gained attention. Studies with laboratory-cultivated methanogens elucidate the transformation of inorganic mercury (Hg) into MeHg, thereby uncovering underlying microbial methylation mechanisms. However, this field faces challenges such as significant Hg loss and unstable culture systems, which impede accurate assessment of these processes. This study aims to develop a reliable low-Hg-loss cultivation protocol for Hg methylati…

Impact of dietary fibre:starch ratio in shaping caecal archaea revealed in rabbits.

In rabbits, many studies have investigated the effect of diet, including the fibre intake, on caecal microbiota; however, there are no direct measurements of the influence of diets with different dietary fibre-to-starch ratios and the archaeal community composition in the caecum. We used 16S rDNA sequencing to investigate the impact of different dietary neutral detergent fibre (NDF)-to-starch ratios (1.0-2.3) on the caecal archaeal community in rabbits. The results revealed that the archaeal community from all experimental rabbits was relatively less complex than intestinal bacterial community…

Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment.

Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. Recent research results show that ammonia-oxidizing archaea (AOA) are both abundant and diverse in a range of ecosystems. In this study, we examined the abundance and diversity of AOA and ammonia-oxidizing beta-proteobacteria (AOB) in estuarine sediments in Hong Kong for two seasons using the ammonia monooxygenase A subunit gene (amoA) as molecular biomarker. Relationships between diversity and abundance of AOA and AOB and physicochemical parameters were also explored. AOB were more diverse but less abundant than …

Distribution of Archaea in Japanese patients with periodontitis and humoral immune response to the components.

There is controversy regarding the existence of archaeal pathogens. Periodontitis is one of the human diseases in which Archaea have been suggested to have roles as pathogens. This study was performed to investigate the distribution of Archaea in Japanese patients with periodontitis and to examine the serum IgG responses to archaeal components. Subgingival plaque samples were collected from 111 periodontal pockets of 49 patients (17 with aggressive periodontitis and 32 with chronic periodontitis), and 30 subgingival plaque samples were collected from 17 healthy subjects. By PCR targeting the 1…

Nonspecific adherence by Actinobacillus actinomycetemcomitans requires genes widespread in bacteria and archaea.

The gram-negative coccobacillus, Actinobacillus actinomycetemcomitans, is the putative agent for localized juvenile periodontitis, a particu … imal pathogen Pasteurella multocida. Partial tad loci also occur in strikingly diverse Bacteria and Archaea. Our results show that the tad genes are required for tight adherence of A. actinomycetemcomitans to surfaces and are therefore likely to be essential for colonization and pathogenesis. The occurrence of similar genes in a wide array of microorganis …

High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.

Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7 ± 15

Halophilic bacteria and archaea in salinity-resilient agriculture: mechanisms and multi-omics perspectives.

Soil salinization due to anthropogenic activity and climate change is a bottleneck to the global agricultural yield and food security. Conventional approaches for mitigating salt stress, including utilization of chemical fertilizers, have shown limited success, and the use of genetically engineered microbes as bioinoculants or salt-tolerant crop varieties against abiotic salinity stress often faces regulatory challenges with extended timelines. Contrary to the existing approaches, employment of halophilic bacteria and archaea offers a promising platform for eco-friendly and sustainable crop cu…

L-Asparaginase Conjugates from the Hyperthermophilic Archaea Thermococcus sibiricus with Improved Biocatalytic Properties.

This study investigated the effect of polycationic and uncharged polymers (and oligomers) on the catalytic parameters and thermostability of L-asparaginase from Thermococcus sibiricus (TsA). This enzyme has potential applications in the food industry to decrease the formation of carcinogenic acrylamide during the processing of carbohydrate-containing products. Conjugation with the polyamines polyethylenimine and spermine (PEI and Spm) or polyethylene glycol (PEG) did not significantly affect the secondary structure of the enzyme. PEG contributes to the stabilization of the dimeric form of TsA,

Структурный анализ процесса сбора света с помощью антенн, содержащих родопсины в морской архееи Асгарда.

Акватические бактериальные редопсиновые протонные насосы собирают световую энергию для фотогетертрофного роста и, как известно, содержат гидроксилированные каротеи, расширяющие волны используемого света, но они не характеризуются морской археей. Здесь, комбинируя морскую хромофорную экстракт с очищенными архейскими родопсинами, выявленными в морских метагеномах, мы показываем передачу легкой энергии из различных гидроксилоидных каротеоидных в геймдаллархаэ (HeimdallRs) из некультурных морских планктонных членов «Candidatus Cariarachaeceae» (Candidatus Asgardarchaeota). Эти светообрабатывающие

Совпадение в аннотации оригинала
Aquatic bacterial rhodopsin proton pumps harvest light energy for photoheterotrophic growth and are known to contain hydroxylated carotenoids that expand the wavelengths of light utilized, but these have not been characterized in marine archaea. Here, by combining a marine chromophore extract with purified archaeal rhodopsins identified in marine metagenomes…

Advancing anaerobic microbial studies with in situ Raman spectroscopy: Methanogenic archaea as a model.

Methanogenic archaea play a critical role in methane (CH4) production and the global carbon cycle, yet accurately monitoring their gas metabolism under anaerobic conditions remains a technical challenge. In this study, we developed a Raman spectroscopy-based gas quantification model, achieving high-precision monitoring of CO2-N2-CH4 ternary gas mixtures over a temperature range of 12-52 °C. The model exhibited strong linear correlations between the Raman peak area ratios and gas molar ratios, which were further validated against gas chromatography, revealing no significant differences (p > 0.0…

Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica.

The halophilic archaeon Haloarcula hispanica utilizes the sugar alcohols mannitol and sorbitol as carbon and energy sources. Genes, enzymes, and transcriptional regulators involved in uptake and degradation of these sugar alcohols were identified by growth experiments with deletion mutants and enzyme characterization. It is shown that both mannitol and sorbitol are taken up via a single ABC transporter of the CUT1 transporter family. Then, mannitol and sorbitol are oxidized to fructose by two distinct dehydrogenases. Fructose is further phosphorylated to fructose-1-phosphate by a haloarchaeal …

Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity.

The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens-especially those focused on children-are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn's disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity as…

Metabolic potential of anaerobic methane oxidizing archaea for a broad spectrum of electron acceptors.

Methane (CH4) is a potent greenhouse gas significantly contributing to the climate warming we are currently facing. Microorganisms play an i … as well as biochar and perchlorate (ClO4-) were suggested to mediate AOM. Anaerobic methanotrophic archaea, the so-called ANME archaea, are key players in the AOM process, yet we are still lacking deeper understanding of their metabolism, electron acceptor preferences and their interaction with other microbial community members. It is still not clear whe …

Correction: Biochemical and genetic studies define the functions of methylthiotransferases in methanogenic and methanotrophic archaea.

[This corrects the article DOI: 10.3389/fmicb.2023.1304671.].

ThiN as a versatile domain of transcriptional repressors and catalytic enzymes of thiamine biosynthesis in archaea.

Thiamine pyrophosphate (TPP), the active form of vitamin B1, is a cofactor required for catalyzing key reactions in carbohydrate and amino a … aracterized in certain bacteria, plants and fungi, these pathways are comparatively understudied in archaea. Recent work reveals archaeal thiamine metabolism to be chimeric, combining eukaryotic THI4-dependent thiazole formation with bacterial ThiC-mediated pyrimidine synthesis. Moreover, archaeal thiamine synthesis can be regulated by a ThiN-domain-depen …

Role of alcohols in growth, lipid composition, and membrane fluidity of yeasts, bacteria, and archaea.

Increased membrane fluidity, which causes cofactor leakage and loss of membrane potential, has long been documented as a cause for decreased cell growth during exposure to ethanol, butanol, and other alcohols. Reinforcement of the membrane with more complex lipid components is thus thought to be beneficial for the generation of more tolerant organisms. In this study, organisms with more complex membranes, namely, archaea, did not maintain high growth rates upon exposure to alcohols, indicating that more complex lipids do not necessarily fortify the membrane against the fluidizing effects of al…

A novel Arabidopsis gene required for ethanol tolerance is conserved among plants and archaea.

A novel ethanol-hypersensitive mutant, gek1, of Arabidopsis shows 10-100 times greater sensitivity to ethanol compared to the wild type, whi … nterestingly, a similarity search revealed that GEK1-related genes are conserved only in plants and archaea. These results might suggest that plants, and presumably archaea, have a novel mechanism for protection from acetaldehyde toxicity.

Methanogenic archaea Methanobrevibacter smithii and Methanosphaera stadtmanae promote mucosal homeostasis and protect from colitis.

The intestinal microbiota is a critical determinant of mucosal homeostasis, yet the functional contributions of Archaea-which constitute up to 10% of the anaerobic community-remain largely undefined. Here, we provide evidence that the human methanogens Methanobrevibacter smithii (MSm) and Methanosphaera stadtmanae (MSt) promote colonic health. Transcriptomic analysis of germ-free mice reveals that MSm and MSt induce distinct colonic programs important for epithelial integrity. Using gnotobiotic and antibiotic-treated specific-pathogen-free mouse models, we show that MSm and MSt reinforce the e…