@article {pmid40340443,
year = {2025},
author = {Díaz-Rullo, J and González-Pastor, JE},
title = {Molecular adaptations specific to extreme halophilic archaea could promote high perchlorate tolerance.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0051225},
doi = {10.1128/aem.00512-25},
pmid = {40340443},
issn = {1098-5336},
abstract = {Perchlorate is a strong chaotropic agent that causes macromolecule denaturation, DNA damage, and oxidative stress. However, perchlorate deliquescence is thought to promote the formation of liquid salt brines, even at hyper-arid and cold environments, such as the Martian regolith. For that reason, the detection of high levels of perchlorate at different locations on the Martian surface led to hypotheses about the existence of Martian microenvironments compatible with life, especially with those organisms tolerant to hyper-salinity and perchlorate. Extreme halophilic archaea have been proposed as the best candidates to inhabit those environments not only due to their high tolerance to salinity and perchlorate, but also because of their resistance to a wide variety of stress conditions. Since specific perchlorate responses remain largely unknown, in this work, we have analyzed the molecular mechanisms of perchlorate tolerance exhibited by the model extreme halophilic archaeon Haloferax volcanii using a transcriptomic approach. We report that perchlorate produced transcriptional effects opposite to those of salinity, and we propose that the "salt-in" strategy could promote high perchlorate tolerance in extreme halophilic archaea due to the intracellular accumulation of KCl, which may shield the chaotropic activity of perchlorate. This natural adaptation would be enhanced by changes in other stress responses like DNA repair, refolding and turnover of damaged proteins, removal of oxidative species, and tRNA modifications, among others. These results may help to understand how life could survive on Mars, now or in the past, and highlight the importance of extreme halophiles in the development of in situ resource utilization systems.IMPORTANCEPerchlorate is a toxic chlorinated compound that promotes the formation of liquid salt brines, even at hyper-arid and cold environments. For the past two decades, different probes have reported high levels of perchlorate salts at multiple locations on the Martian surface, which could facilitate the presence of potentially habitable environments by specific microorganisms capable of tolerating both hyper-salinity and high perchlorate concentrations. Therefore, the significance of this research was to investigate the molecular mechanisms for perchlorate tolerance using the extreme haloarchaeon Haloferax volcanii as a model organism. This analysis leads to the identification of critical genes and pathways involved in perchlorate tolerance and supports that certain molecular adaptations specific to extreme haloarchaea may be responsible for the high levels of perchlorate tolerance exhibited by these microorganisms, serving as a valuable resource for Mars exploration.},
}

@article {pmid40339316,
year = {2025},
author = {Cuzman, OA and Raio, A and Galeotti, M and Striova, J and Chaban, A and Innocenti, S and Penoni, S and de Luca, F and Cantini, B and Petrocchi, D},
title = {Pink discoloration due to pigmented Archaea on the walls of the so-called Michelangelo's "secret room" (Medici Chapel, Florence, Italy).},
journal = {The Science of the total environment},
volume = {981},
number = {},
pages = {179494},
doi = {10.1016/j.scitotenv.2025.179494},
pmid = {40339316},
issn = {1879-1026},
abstract = {Pink discolorations are often observed on heritage buildings mainly in areas affected by salt weathering, where the development of halotolerant and halophilic microorganisms is favored. Part of these extremophilic microorganisms contains carotenoids, reason for which their colonization becomes visible by naked eye on large surfaces. This work investigates the pink alteration of the walls with drawings attributed to Michelangelo, located in the basement room of the Medici Chapel (Florence, Italy). The results of in-depth multidisciplinary investigations are discussed in the context of a thorough literature review on pink alterations of heritage buildings. For the first time, we combined culture-based approaches with metagenomic analyses that revealed the pink pigmented archaea Halalkalicoccus sp. as dominant, pointing their role in the pink discoloration present on the wall. Raman spectroscopy was exploited for the characterization of the biogenic pigments and Fourier Transform infrared spectroscopy and scanning electron microscopy to analyze the salt formations present on the walls.},
}

@article {pmid40320202,
year = {2025},
author = {Gordon, R},
title = {A Call for Research on the Basis for Polygonal Pleomorphism in Archaea.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105478},
doi = {10.1016/j.biosystems.2025.105478},
pmid = {40320202},
issn = {1872-8324},
abstract = {Morphogenesis is a major unsolved problem. It is usually tackled in the embryogenesis of multicellular organisms, but rarely leans on studies of single-cell organisms. But the latter often have fascinating, puzzling shapes, whose understanding may be key to multicellular embryogenesis, wound healing, and regeneration. Here, I call for new directions in studying what may have been the first shaped, single-celled organisms, the Domain of Archaea, which might have been LUCA (Last Universal Common Ancestor), the first organisms at the origin of life. While their shaping is usually attributed to the "crystallinity" of the S-layer, this may have the liquidity of a bubble raft.},
}

@article {pmid40320078,
year = {2025},
author = {Zuo, A and Ba, Y and Liu, S and Shan, D and Liu, Z},
title = {Gut Archaea in Colorectal Cancer Diagnosis and Ecology.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2024.11.036},
pmid = {40320078},
issn = {1528-0012},
}

@article {pmid40313972,
year = {2025},
author = {Sun, J and Zhou, H and Cheng, H and Chen, Z and Wang, Y},
title = {Archaea show different geographical distribution patterns compared to bacteria and fungi in Arctic marine sediments.},
journal = {mLife},
volume = {4},
number = {2},
pages = {205-218},
pmid = {40313972},
issn = {2770-100X},
abstract = {Microorganisms dominate marine environments in the polar oceans and are known to harbor greater diversity and abundance than was once thought, and yet, little is known about their biogeographic distribution patterns in marine sediments at a broad spatial scale. In this study, we conducted extensive sampling of marine sediments along a latitudinal transect spanning 2500 km from the Bering Sea to the Arctic Ocean to investigate the geographical distribution patterns of bacteria, archaea, and fungi. Our findings revealed that the community similarities of bacteria and fungi decay at similar rates with increasing geographical distance (slope: -0.005 and -0.002), which are much lower than the decay rate of archaeal communities (slope: -0.012). Notably, microbial richness and community composition showed significant differences in the region of 75-80°N compared to other regions in 60-75°N. Salinity, temperature, pH, ammonium nitrogen, and total organic carbon are key factors that significantly affect microbial community variations. Furthermore, bacterial co-occurrence networks showed more complex interactions but lower modularity than fungal counterparts. This study provides crucial insights into the spatial distribution patterns of bacteria, archaea, and fungi in the Arctic marine sediments and will be critical for a better understanding of microbial global distribution and ecological functions.},
}

@article {pmid40275524,
year = {2025},
author = {Ma, W and Lin, M and Shen, P and Chi, H and Zhang, W and Zhu, J and Tian, S and Liu, P},
title = {Exploring methanogenic archaea and their thermal responses in the glacier-fed stream sediments of Rongbuk River basin, Mt. Everest.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {5},
pages = {},
pmid = {40275524},
issn = {1574-6941},
support = {42171144//National Natural Science Foundation of China/ ; 42222105//Excellent Young Scientists Fund/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Rivers/microbiology ; *Archaea/metabolism/classification/genetics ; Carbon Dioxide/metabolism ; Temperature ; Altitude ; China ; Phylogeny ; },
abstract = {Glacier-fed streams (GFS) are emergent sources of greenhouse gas methane, and methanogenic archaea in sediments contribute largely to stream methane emissions. However, little is known about the methanogenic communities in GFS sediments and their key environmental driving factors. This study analyzed stream sediments from the Rongbuk River basin on Mt. Everest for methanogenic communities and their temperature responses through anaerobic microcosm incubations at 5°C and 15°C. Diverse methanogens were identified, including acetoclastic, hydrogenotrophic, and hydrogen-dependent methylotrophic types. Substantial methane and CO2 production were detected across altitudes and increased significantly at 15°C, with both methane and CO2 production rates negatively correlated with altitude. The temperature sensitivity of CO2 production also showed a negative altitude correlation. Methanogens increased substantially over long-term incubation, dominating the archaeal community. At 15°C, the relative abundance of several methanogenic groups was strongly correlated with altitude, with positive correlations observed for Methanomassiliicoccaceae and Methanoregulaceae, and negative correlations for Methanocellaceae, respectively. Besides altitude, phosphorus, carbon to nitrogen ratio, and pH also affected methanogenic structure, methane and CO2 production, and temperature sensitivities. This study offers new insights into methanogens and methane production in GFS sediments, improving our understanding of GFS carbon cycling and its potential responses to climate change.},
}

*Methane/metabolism
*Geologic Sediments/microbiology
*Rivers/microbiology
*Archaea/metabolism/classification/genetics
Carbon Dioxide/metabolism
Temperature
Altitude
China
Phylogeny

@article {pmid40181255,
year = {2025},
author = {Mohammadzadeh, R and Mahnert, A and Shinde, T and Kumpitsch, C and Weinberger, V and Schmidt, H and Moissl-Eichinger, C},
title = {Age-related dynamics of predominant methanogenic archaea in the human gut microbiome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {193},
pmid = {40181255},
issn = {1471-2180},
support = {P 32697//Austrian Science Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Aged ; *Archaea/classification/genetics/metabolism/isolation & purification ; *Methane/metabolism ; Feces/microbiology ; Aged, 80 and over ; Young Adult ; Female ; Male ; *Aging ; Age Factors ; Methanobrevibacter/genetics ; Metagenomics ; Phylogeny ; Bacteria/classification/genetics/metabolism ; },
abstract = {BACKGROUND: The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.

METHODS: Shotgun metagenomic data from the stool samples of young adults (n = 127, Age: 19-59 y), older adults (n = 86, Age: 60-99 y), and centenarians (n = 34, age: 100-109 years) were analyzed.

RESULTS: Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in Methanobrevibacter smithii, rather than Candidatus Methanobrevibacter intestini. Remarkably, Ca. M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for M. smithii in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with Oscillospiraceae.

CONCLUSIONS: This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both M. smithii and Ca. M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.},
}

Humans
*Gastrointestinal Microbiome
Middle Aged
Adult
Aged
*Archaea/classification/genetics/metabolism/isolation & purification
*Methane/metabolism
Feces/microbiology
Aged, 80 and over
Young Adult
Female
Male
*Aging
Age Factors
Methanobrevibacter/genetics
Metagenomics
Phylogeny
Bacteria/classification/genetics/metabolism

@article {pmid40180612,
year = {2025},
author = {Song, ZM and Cai, C and Gao, Y and Lin, X and Yang, Q and Zhang, D and Wu, G and Liang, H and Zhuo, Q and Zhang, J and Cai, P and Jiang, H and Liu, W and Li, YX},
title = {Decoding the Chemical Language of Ribosomally Synthesized and Post-Translationally Modified Peptides from the Untapped Archaea Domain.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202501074},
doi = {10.1002/anie.202501074},
pmid = {40180612},
issn = {1521-3773},
abstract = {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 twenty-four 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.},
}

@article {pmid40179202,
year = {2025},
author = {Pillai, EK and Brunet, T},
title = {Archaea go multicellular under pressure.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {28-29},
doi = {10.1126/science.adw6689},
pmid = {40179202},
issn = {1095-9203},
mesh = {*Archaea/physiology/cytology ; },
abstract = {A microbe from the Dead Sea switches to a tissue-like form when compressed.},
}

*Archaea/physiology/cytology

@article {pmid40179183,
year = {2025},
author = {Rados, T and Leland, OS and Escudeiro, P and Mallon, J and Andre, K and Caspy, I and von Kügelgen, A and Stolovicki, E and Nguyen, S and Patop, IL and Rangel, LT and Kadener, S and Renner, LD and Thiel, V and Soen, Y and Bharat, TAM and Alva, V and Bisson, A},
title = {Tissue-like multicellular development triggered by mechanical compression in archaea.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {109-115},
doi = {10.1126/science.adu0047},
pmid = {40179183},
issn = {1095-9203},
mesh = {Actins/metabolism ; Archaeal Proteins/metabolism ; Glycosylation ; Elasticity ; Biological Evolution ; Biomechanical Phenomena ; Stress, Mechanical ; },
abstract = {The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal multicellularity in haloarchaea, forming tissue-like structures. These archaeal tissues are mechanically and molecularly distinct from their unicellular lifestyle, mimicking several eukaryotic features. Archaeal tissues undergo a multinucleate stage followed by tubulin-independent cellularization, orchestrated by active membrane tension at a critical cell size. After cellularization, tissue junction elasticity becomes akin to that of animal tissues, giving rise to two cell types-peripheral (Per) and central scutoid (Scu) cells-with distinct actin and protein glycosylation polarity patterns. Our findings highlight the potential convergent evolution of a biophysical mechanism in the emergence of multicellular systems across domains of life.},
}

Actins/metabolism
Archaeal Proteins/metabolism
Glycosylation
Elasticity
Biological Evolution
Biomechanical Phenomena
Stress, Mechanical

@article {pmid40170918,
year = {2025},
author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T},
title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549128},
pmid = {40170918},
issn = {1664-302X},
abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.},
}

@article {pmid40169898,
year = {2025},
author = {Schmerling, C and Schroeder, C and Zhou, X and Bost, J and Waßmer, B and Ninck, S and Busche, T and Montero, L and Kaschani, F and Schmitz, OJ and Kalinowski, J and Kaiser, M and Albers, SV and Bräsen, C and Siebers, B},
title = {An unusual glycerol-3-phosphate dehydrogenase in Sulfolobus acidocaldarius elucidates the diversity of glycerol metabolism across Archaea.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {539},
pmid = {40169898},
issn = {2399-3642},
support = {BMBF 031B0848A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
mesh = {*Glycerol/metabolism ; *Sulfolobus acidocaldarius/enzymology/genetics/metabolism ; *Glycerolphosphate Dehydrogenase/metabolism/genetics ; Archaeal Proteins/metabolism/genetics ; Archaea/genetics/metabolism/enzymology ; Phylogeny ; },
abstract = {Glycerol is highly abundant in natural ecosystems and serves as both an important carbon source for microorganisms as well as a promising feedstock for industrial applications. However, the pathways involved in glycerol degradation in Archaea remain unclear. Here, we show that the thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius can grow with glycerol as its sole carbon source and characterize the mechanisms involved in glycerol utilization. We show that after uptake involving facilitated diffusion, glycerol is phosphorylated to glycerol-3-phosphate by glycerol kinase (GK), followed by oxidation to dihydroxyacetone phosphate catalyzed by an unusual glycerol-3-phosphate dehydrogenase (G3PDH) with a previously undescribed type of membrane anchoring via a CoxG-like protein. Furthermore, we show that while S. acidocaldarius has two paralogous GK/G3PDH copies (saci_1117-1119, saci_2031-2033) with similar biochemical activity, only saci_2031-2033 is highly upregulated and essential on glycerol, suggesting that distinct enzyme pairs may be regulated by different environmental conditions. Finally, we explore the diversity of glycerol metabolism enzymes across the Archaea domain, revealing a high versatility of G3PDHs with respect to interacting proteins, electron transfer mechanisms, and modes of membrane anchoring. Our findings help to elucidate the mechanisms involved in glycerol utilization in Archaea, highlighting unique evolutionary strategies that likely enabled adaptation to different lifestyles.},
}

*Glycerol/metabolism
*Sulfolobus acidocaldarius/enzymology/genetics/metabolism
*Glycerolphosphate Dehydrogenase/metabolism/genetics
Archaeal Proteins/metabolism/genetics
Archaea/genetics/metabolism/enzymology
Phylogeny

@article {pmid40162572,
year = {2025},
author = {Wu, H and Zhang, H and Dong, T and Li, Z and Guo, X and Chen, H and Yao, Y},
title = {Overcoming Extreme Ammonia Inhibition on Methanogenesis by Artificially Constructing a Synergistically Community with Acidogenic Bacteria and Hydrogenotrophic Archaea.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2502743},
doi = {10.1002/advs.202502743},
pmid = {40162572},
issn = {2198-3844},
support = {2024YFD1700500//National Key R&D Program of China/ ; A279021901//Shaanxi Youth Thousand Talents/ ; 2024CY2-GJHX-74//Shaanxi Key R&D Program of China/ ; 2452021112//Chinese Universities Scientific Fund/ ; JCYJ20220530161408019//Shenzhen Natural Science Foundation/ ; 2023KCXTD038//Guangdong Provincial University Innovation Team Project/ ; 2022-K32//Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering/ ; Z111021902//Northwest A&F University Young Talent Project/ ; },
abstract = {High total ammonia nitrogen (TAN) inhibits anaerobic digestion (AD) and cannot be completely eliminated by merely enhancing a stage of AD. This study incorporates TAN-tolerant inoculum into substrates hydrolyzed by Rhizopus mixed agents to simultaneously enhance hydrolysis-acidogenesis-methanogenesis. The results show a 16.46-fold increase in CH4 production under TAN-inhibited (6870.97 mg L-1) conditions, even exceeding the AD without TAN by 21.10%. Model substrates sodium acetate and mixed H2 confirm hydrogenotrophic methanogenesis is the main pathway, with reduced TAN inhibition. Furthermore, a synergistic metabolic microbial community dominated by hydrolytic bacteria JAAYGG01 sp. and DTU014 sp., acidogenic bacteria DTU015 sp., DTU013 sp., and JAAYLO01 sp., and methanogens Methanosarcina mazei and an unclassified species in the Methanoculleus is reconstructed to resist TAN inhibition. Metagenomic combined with metatranscriptomic sequencing identifies that this microbial community carries xynD and bglB to regulate substrate hydrolysis, leading to acetate production through glycolysis, butyrate, and pyruvate metabolism with high acetate kinase activity, thereby CH4 produced primarily via hydrogenotrophic methanogenesis with high coenzyme F420 activity, facilitated by efficient mass transfer processes and quorum sensing regulation. This cleaner strategy obtains higher economic benefit (US$149.02) than conventional AD and can increase 154.64-fold energy production of a 24 000 m3 biogas plant, guided by machine learning.},
}

@article {pmid40156577,
year = {2025},
author = {Kop, LFM and Koch, H and Martins, PD and Suarez, C and Karačić, S and Persson, F and Wilén, BM and Hagelia, P and Jetten, MSM and Lücker, S},
title = {High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf032},
pmid = {40156577},
issn = {1574-6941},
abstract = {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% but a wide range between 1.2-61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome (MAG) analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.},
}

@article {pmid40149641,
year = {2025},
author = {Bruno, PS and Biggers, P and Nuru, N and Versaci, N and Chirila, MI and Darie, CC and Neagu, AN},
title = {Small Biological Fighters Against Cancer: Viruses, Bacteria, Archaea, Fungi, Protozoa, and Microalgae.},
journal = {Biomedicines},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/biomedicines13030665},
pmid = {40149641},
issn = {2227-9059},
support = {R15CA260126/CA/NCI NIH HHS/United States ; },
abstract = {Despite the progress made in oncological theranostics, cancer remains a global health problem and a leading cause of death worldwide. Multidrug and radiation therapy resistance is an important challenge in cancer treatment. To overcome this great concern in clinical practice, conventional therapies are more and more used in combination with modern approaches to improve the quality of patients' lives. In this review, we emphasize how small biological entities, such as viruses, bacteria, archaea, fungi, protozoans, and microalgae, as well as their related structural compounds and toxins/metabolites/bioactive molecules, can prevent and suppress cancer or regulate malignant initiation, progression, metastasis, and responses to different therapies. All these small biological fighters are free-living or parasitic in nature and, furthermore, viruses, bacteria, archaea, fungi, and protozoans are components of human and animal microbiomes. Recently, polymorphic microbiomes have been recognized as a new emerging hallmark of cancer. Fortunately, there is no limit to the development of novel approaches in cancer biomedicine. Thus, viral vector-based cancer therapies based on genetically engineered viruses, bacteriotherapy, mycotherapy based on anti-cancer fungal bioactive compounds, use of protozoan parasite-derived proteins, nanoarchaeosomes, and microalgae-based microrobots have been more and more used in oncology, promoting biomimetic approaches and biology-inspired strategies to maximize cancer diagnostic and therapy efficiency, leading to an improved patients' quality of life.},
}

@article {pmid40142528,
year = {2025},
author = {Di Naro, M and Petronio Petronio, G and Mukhtar, F and Cutuli, MA and Magnifico, I and Falcone, M and Brancazio, N and Guarnieri, A and Di Marco, R and Nicolosi, D},
title = {Extracellular Vesicles in Bacteria, Archaea, and Eukaryotes: Mechanisms of Inter-Kingdom Communication and Clinical Implications.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
pmid = {40142528},
issn = {2076-2607},
abstract = {Living organisms must adapt and communicate effectively in their environment to survive. Cells communicate through various mechanisms, including releasing growth factors, chemokines, small bioactive molecules, and cell-cell contact. In recent years, a new and sophisticated cell communication mechanism based on extracellular vesicles (EVs) has been described in all three domains of life: archaea, bacteria, and eukaryotes. EVs are small, bilayer proteolipid vesicles released by cells into the extracellular space. This review aims to analyze and compare the current literature on bacterial, archaeal, and eukaryotic EVs and their possible clinical applications. This framework will address three key points: (a) The role of EVs in bacteria, eukaryotes, and archaea. (b) What is the impact of EVs in archaea on disease?},
}

@article {pmid40130855,
year = {2025},
author = {Lyu, X and Yu, H and Lu, Y},
title = {Diversity and function of soluble heterodisulfide reductases in methane-metabolizing archaea.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0323824},
doi = {10.1128/spectrum.03238-24},
pmid = {40130855},
issn = {2165-0497},
abstract = {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.},
}

@article {pmid40120574,
year = {2025},
author = {Wollweber, F and Xu, J and Ponce-Toledo, RI and Marxer, F and Rodrigues-Oliveira, T and Pössnecker, A and Luo, ZH and Malit, JJL and Kokhanovska, A and Wieczorek, M and Schleper, C and Pilhofer, M},
title = {Microtubules in Asgard archaea.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.02.027},
pmid = {40120574},
issn = {1097-4172},
abstract = {Microtubules are a hallmark of eukaryotes. Archaeal and bacterial homologs of tubulins typically form homopolymers and non-tubular superstructures. The origin of heterodimeric tubulins assembling into microtubules remains unclear. Here, we report the discovery of microtubule-forming tubulins in Asgard archaea, the closest known relatives of eukaryotes. These Asgard tubulins (AtubA/B) are closely related to eukaryotic α/β-tubulins and the enigmatic bacterial tubulins BtubA/B. Proteomics of Candidatus Lokiarchaeum ossiferum showed that AtubA/B were highly expressed. Cryoelectron microscopy structures demonstrate that AtubA/B form eukaryote-like heterodimers, which assembled into 5-protofilament bona fide microtubules in vitro. The additional paralog AtubB2 lacks a nucleotide-binding site and competitively displaced AtubB. These AtubA/B2 heterodimers polymerized into 7-protofilament non-canonical microtubules. In a sub-population of Ca. Lokiarchaeum ossiferum cells, cryo-tomography revealed tubular structures, while expansion microscopy identified AtubA/B cytoskeletal assemblies. Our findings suggest a pre-eukaryotic origin of microtubules and provide a framework for understanding the fundamental principles of microtubule assembly.},
}

@article {pmid40120250,
year = {2025},
author = {Mahayri, TM and Mrázek, J and Bovera, F and Piccolo, G and Murgia, GA and Moniello, G and Fliegerová, KO},
title = {The inclusion of insect meal from Hermetia illucens larvae in the diet of laying hens (Hy-line Brown) affects the caecal diversity of methanogenic archaea.},
journal = {Poultry science},
volume = {104},
number = {5},
pages = {105037},
doi = {10.1016/j.psj.2025.105037},
pmid = {40120250},
issn = {1525-3171},
abstract = {The effect of the dietary inclusion of Hermetia illucens larvae meal on the diversity of the methanogenic archaea in the caecum of laying hens (Hy-line Brown) was investigated using molecular methods. A total of 27 hens, selected equally for slaughter from 162 birds which were divided equally into 3 treatment groups including control group C with a diet containing corn-soybean meal and 2 experimental groups, HI25 and HI50, in which 25% and 50% of the soybean meal protein was replaced by the protein from a Hermetia illucens larvae meal, respectively. At 40 weeks of age, the methanogenic community of caecal content of 9 hens per group was analyzed using a 16S rRNA gene clone library. A total of 108 positive clones, 35 from the control group, 44 from the HI25 group and 29 from the HI50 group, were analyzed by Sanger sequencing. Methanomicrobiales, Methanobacteriales and Methanomassiliicoccales were the main orders found in groups C and HI25. Methanomassiliicoccales was absent in the HI50 group, which was dominated by the order Methanobacteriales. At the species level, Methanobrevibacter woesei was the most prevalent species in all three groups regardless of diet. Some species were found exclusively either in the control group (Methanogenic archaeon CH1270) or in the HI25 group (Methanorbis furvi strain Ag1). Methanogenic diversity was significantly lower in the HI50 group compared to the control and HI25 groups and Methanomassiliicoccaceae archaeon DOK was completely suppressed in HI50 group. Our preliminary results indicate that ingestion of Hermetia illucens larvae meal has considerable effect on the methanogenic community, promoting the abundance of Methanobrevibacter woesei and suppressing Methanomassiliicoccaceae archaeon DOK in the caeca of laying hens.},
}

@article {pmid40088845,
year = {2025},
author = {Zhuo, J and Zheng, R and Luan, Z and Li, L and Xi, S and Du, Z and He, W and Sun, C and Zhang, X},
title = {Advancing anaerobic microbial studies with in situ Raman spectroscopy: Methanogenic archaea as a model.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {336},
number = {},
pages = {126043},
doi = {10.1016/j.saa.2025.126043},
pmid = {40088845},
issn = {1873-3557},
abstract = {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 > 0.05). This confirms the reliability and accuracy of the approach.. Building upon this model, we conducted real-time monitoring of the gas metabolism of methylotrophic methanogenic archaea under anaerobic conditions. The results demonstrated that methanol concentration significantly influenced the gas production kinetics. At a methanol concentration of 10 μL/mL, the highest CH4 yield (59.97 %) was achieved, along with stable metabolic activity. In contrast, higher concentrations caused substrate saturation effects, leading to decreased metabolic efficiency. Furthermore, by integrating Raman spectroscopy with high-precision pressure monitoring, this study successfully achieved real-time molar quantification of CH4 and CO2 during methanogen cultivation. This approach provided detailed insights into gas production dynamics and substrate utilization patterns. Compared to traditional methods, this non-destructive, real-time monitoring platform offers a novel tool for anaerobic metabolism research and lays a solid foundation for applications in biogas optimization, industrial fermentation, and renewable energy development.},
}

@article {pmid40070055,
year = {2025},
author = {Klein, T and Hodgskiss, LH and Dreer, M and Murrell, JC and Hutchings, MI and Schleper, C and Lehtovirta-Morley, LE},
title = {Distinct Patterns of Antibiotic Sensitivities in Ammonia-Oxidising Archaea.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70063},
pmid = {40070055},
issn = {1462-2920},
support = {ActionR 101079299//HORIZON EUROPE European Research Council/ ; UNITY 852993/ERC_/European Research Council/International ; W1257//Austrian Science Fund/ ; NE/S007334/1//Natural Environment Research Council/ ; DH150187//Royal Society/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; *Archaea/genetics/drug effects/metabolism ; *Ammonia/metabolism ; Oxidation-Reduction ; Microbial Sensitivity Tests ; },
abstract = {Ammonia-oxidising archaea (AOA) are important microorganisms contributing towards the nitrogen flux in the environment. Unlike archaea from other major phyla, genetic tools are yet to be developed for the AOA, and identification of antibiotic resistance markers for selecting mutants is required for a genetic system. The aim of this study was to test the effects of selected antibiotics (hygromycin B, neomycin, apramycin, puromycin, novobiocin) on pure cultures of three well studied AOA strains, 'Candidatus Nitrosocosmicus franklandianus C13', Nitrososphaera viennensis EN76 and Nitrosopumilus maritimus SCM1. Puromycin, hygromycin B and neomycin inhibited some but not all tested archaeal strains. All strains were resistant to apramycin and inhibited by novobiocin to various degrees. As N. viennensis EN76 was relatively more resistant to the tested antibiotics, a wider range of concentrations and compounds (chloramphenicol, trimethoprim, statins) was tested against this strain. N. viennensis EN76 was inhibited by trimethoprim, but not by chloramphenicol, and growth recovered within days in the presence of simvastatin, suggesting either degradation of, or spontaneous resistance against, this compound. This study highlights the physiological differences between different genera of AOA and has identified new candidate antibiotics for selective enrichment and the development of selectable markers for genetic systems in AOA.},
}

*Anti-Bacterial Agents/pharmacology
*Archaea/genetics/drug effects/metabolism
*Ammonia/metabolism
Oxidation-Reduction
Microbial Sensitivity Tests

@article {pmid40068810,
year = {2025},
author = {Carré, L and Natali, F and Zaccai, G and Çumaku, V and Franzetti, B},
title = {Determination of in cellulo proteome molecular dynamics in different halophilic Archaea.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {224},
pages = {20240630},
doi = {10.1098/rsif.2024.0630},
pmid = {40068810},
issn = {1742-5662},
support = {//French National Research Agency/ ; //University Grenoble Alpes graduate school/ ; //Agence Nationale de la Recherche/ ; },
mesh = {*Proteome/metabolism ; *Archaeal Proteins/metabolism/chemistry ; *Molecular Dynamics Simulation ; Archaea/metabolism ; },
abstract = {While biophysical studies have unravelled properties of specific proteins in vitro, characterizing globally their native state within the cell remains a challenge. In particular, protein adaptation to harsh intracellular physical and chemical conditions is poorly understood. Extremophiles, which thrive in severe environments, are good models for the study of such adaptation. Five haloarchaeal species, isolated from hypersaline environments, were used to assess correlations between intracellular salt concentrations and molecular dynamics properties. In cellulo protein stability was measured using nano differential scanning fluorimetry, and neutron spectrometry was used to determine molecular dynamics resilience and global flexibility. It was found that high intracellular accumulation of Mg[2+] and low intracellular accumulation of K[+] were correlated with higher stability and resilience. Sequence traits associated with mean proteome halophilicity, such as decreased hydrophobicity and increased acidity, weighted by the relative abundance of each protein, were also correlated with stability and resilience. Haloferax mediterranei, however, was found to be an exception as its proteome showed the highest in cellulo molecular stability and resilience associated with fewest sequence traits related to halophilicity, highlighting the significance of the intracellular salt environment in determining proteome biophysical properties.},
}

*Proteome/metabolism
*Archaeal Proteins/metabolism/chemistry
*Molecular Dynamics Simulation
Archaea/metabolism

@article {pmid40050166,
year = {2025},
author = {Li, J and Liang, Y and Dong, X},
title = {Post-transcriptional regulation in archaea.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.02.004},
pmid = {40050166},
issn = {1878-4380},
abstract = {During genetic information transfer from DNA to protein, gene expression is strictly controlled at several key stages. Post-transcriptional regulation provides a plethora of mechanisms for precise and rapid control of gene expression, ensuring cellular survival and environmental adaptation. Emerging evidence shows that Archaea, the third domain of life, employ diverse post-transcriptional regulation strategies, including distinct RNA-associated proteins and small noncoding RNAs (sRNAs), to control gene expression. This review summarizes recent advances in understanding archaeal post-transcriptional regulation, focusing on processes, mechanisms, and physiological significances, and key elements including sRNAs, 5'- or 3'-untranslated regions (5'-UTRs or 3'-UTRs), RNA-binding proteins (RBPs) or chaperones, and ribonucleases, underscoring their crucial roles in optimizing archaeal gene expression for survival and environmental responsiveness.},
}

@article {pmid40037099,
year = {2025},
author = {Badra, M and Freudenthal, J and Dumack, K},
title = {Sludge retention time in anaerobic digestion affects Archaea by a cascade through microeukaryotes.},
journal = {Water research},
volume = {278},
number = {},
pages = {123371},
doi = {10.1016/j.watres.2025.123371},
pmid = {40037099},
issn = {1879-2448},
abstract = {Anaerobic digestion is a crucial process for treating organic waste, such as wastewater sludge, agricultural residues and food waste. While the influence of physicochemical parameters on the prokaryotic community composition in anaerobic digesters has been extensively characterized, the role of biotic interactions in shaping the prokaryotic communities remains poorly understood. This study addresses this knowledge gap by analyzing the complete active microbiome of nine full-scale anaerobic digesters. Our findings reveal that eukaryotes, consisting primarily of protists and fungi, account for approximately 40 % of RNA sequence reads alongside dominant Archaea, indicating their substantial role in the digestion process. Our results suggest that the chosen sludge retention time during anaerobic digestion indirectly affects the archaeal community composition and thus treatment efficacy by cascading through eukaryotes, highlighting their integral role in the system. This study highlights the critical role of eukaryotes in regulating prokaryotic communities and their indirect contribution to the optimization of anaerobic digestion efficiency.},
}

@article {pmid40036997,
year = {2025},
author = {Zhu, LR and Mao, YL and Hu, Y and Sun, YP and Hou, J and Cui, HL},
title = {Genome-based taxonomy of the family Haloarculaceae, proposal of Natronomonadaceae fam. nov., and description of four novel halophilic archaea from two saline lakes and a marine solar saltern.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {3},
pages = {126592},
doi = {10.1016/j.syapm.2025.126592},
pmid = {40036997},
issn = {1618-0984},
abstract = {A new family related to the family Haloarculaceae was proposed and the genus Actinarchaeum was merged into the genus Halocatena through phylogenetic, phylogenomic, and comparative genomic analyses. Four strains KK48[T], YCN56[T], SYNS191[T], and SYNS196[T] with new taxonomic status were isolated from inland saline lakes and a marine solar saltern. According to the comparison of 16S rRNA gene and rpoB' gene sequences, strains KK48[T], YCN56[T], SYNS191[T], and SYNS196[T] showed high sequence similarities to the genera Salinibaculum and Salinirubellus, respectively. The values of average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity between these strains and the species of Salinibaculum and Salinirubellus ranged from 75.3 to 77.7 %, 24.5-25.9 % and 66.3-73.4 %, respectively. These data were well below the threshold for species classification, supporting their placements in new taxa. The major polar lipids of these strains were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether, mannosyl glucosyl diether, and disulfated mannosyl glucosyl diether. Based on the phenotypic, chemotaxonomic, phylogenetic, and phylogenomic properties, strains KK48[T] (= CGMCC 1.19060[T] = JCM 35607[T]), YCN56[T] (= CGMCC 1.62603[T] = JCM 36493[T]), SYNS191[T] (= CGMCC 1.62607[T] = JCM 36494[T]), and SYNS196[T] (= CGMCC 1.62608[T] = JCM 36495[T]) represent four novel species of the genera Salinibaculum and Salinirubellus. And Salinibaculum rarum sp. nov., Salinibaculum salinum sp. nov., Salinibaculum marinum sp. nov., and Salinirubellus litoreus sp. nov. are proposed to accommodate these strains.},
}

@article {pmid40028749,
year = {2025},
author = {Salahi, A and Abd El-Ghany, WA},
title = {A Spotlight on Archaea in Humans, Livestock and Poultry: A Review.},
journal = {Veterinary medicine and science},
volume = {11},
number = {2},
pages = {e70263},
pmid = {40028749},
issn = {2053-1095},
mesh = {Animals ; *Archaea/physiology ; Humans ; *Poultry ; Livestock ; Gastrointestinal Microbiome ; },
abstract = {The microbiota includes prokaryotes (archaea and bacteria) and eukaryotes. Archaea are single-celled prokaryotes and essential part of gut microbiome. Researches on archaea in ruminants and humans are more than mono-gastric. The low abundance of archaea in the gut depends on the method used (metagenomics or meta-transcriptomic) and age of people or poultry. The lack of complete recognition of archaea is due to their small number and method of identifying them (16S rRNA gene primers). The uses of archaea include analytical kit, reduce oil pollution, archaeosomes or drugs production, vaccines agents, lipid carriers in the pharmaceutical industry and molybdenum extraction in the nuclear industry. The nutritional functions of methanogenic archaea including feed utilization (ruminants) and efficiency, hydrogen reducing (human), fat deposition and enhancement of energy harvesting in mice, CAZymes genes, cecal fermentation, syntrophic potential, carotenoid source and improved transit time and appetite and SCFAs production. Archaea acting as antibiotics (produce archaeocins, sulfolobicins and halocin KPS1) and as probiotics (archaeobiotics) can reduce TMAU (trimethylaminuria) disease, cardiovascular diseases (CVDs), and atherosclerosis, brain abscess, cancer, colorectal cancer, inflammatory bowel disease (IBD), constipation, obesity, food allergies, asthma and anti-inflammation which can be prevented by using archaea, and other functions include energy homeostasis, heat shock protein (HSP) production and reducing aging.},
}

Animals
*Archaea/physiology
Humans
*Poultry
Livestock
Gastrointestinal Microbiome

@article {pmid39993224,
year = {2025},
author = {Grossi, V and Cuny, P and Militon, C and Witwinowski, J and Eddhif, B and Sylvi, L and Nowakowski, M and Kosta, A and Antheaume, I and Cornil, J and Dubrac, S and Kende, J and Gribaldo, S and Borrel, G},
title = {Halophilic archaea produce wax esters and use an alternative fatty acyl-CoA reductase for precursor synthesis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf035},
pmid = {39993224},
issn = {1751-7370},
abstract = {Wax esters are fatty acid-based neutral lipids thought to be restricted to bacteria and eukaryotes that play a key role in the functioning and maintenance of cells, especially under adverse conditions. Here we show that several halophilic archaea (Halobacteriales) carry a homologue of the bacterial wax synthase gene. Wax ester synthesis and accumulation is demonstrated in one of these (poly)extremophilic archaea, Natronomonas pharaonis, during growth on long-chain fatty acids. Our bioinformatic analysis also shows that the synthesis of fatty alcohols required for wax ester synthesis could be performed by an enzyme evolutionarily related to class I 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR, classically involved in isoprenoid biosynthesis). Using heterologous expression and enzymatic assays, we show that this HMGR homolog, which we named FcrA (for fatty acyl-CoA reductase), reduces fatty acyl-CoA to fatty alcohol, but cannot reduce 3-hydroxy-3-methylglutaryl-CoA to mevalonate. The conservation of HMGR catalytic residues in FcrA suggests that the two enzymes have a similar catalytic mechanism, whereas an elongated substrate-binding pocket and distinct residues may explain FcrA's selectivity for long chain fatty acyl-CoA. In addition to archaea, FcrA is present in a wide range of bacteria, including ~25% of those predicted to produce wax esters, and accounts for a large proportion of the fatty acyl-CoA reductases found in various environments. Challenging the long-held paradigm that archaea cannot biosynthesize fatty acid-based neutral lipids de novo, this study lays the foundations for further physiological, ecological, and biotechnological investigation of neutral lipid production by systems markedly different from those of eukaryotes and bacteria.},
}

@article {pmid39992937,
year = {2025},
author = {Yanagawa, K and Okabeppu, M and Kikuchi, S and Shiraishi, F and Nakajima, Y and Kano, A},
title = {Vertical distribution of methanotrophic archaea in an iron-rich groundwater discharge zone.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0319069},
doi = {10.1371/journal.pone.0319069},
pmid = {39992937},
issn = {1932-6203},
mesh = {*Groundwater/microbiology/chemistry ; *Methane/metabolism ; *Iron/metabolism ; *Archaea/metabolism/genetics ; *RNA, Ribosomal, 16S/genetics ; *Oxidation-Reduction ; Geologic Sediments/microbiology ; Phylogeny ; Japan ; Anaerobiosis ; },
abstract = {Anaerobic oxidation of methane coupled to iron reduction (Fe-AOM) is a crucial process for methane removal in terrestrial environments. However, the occurrence of Fe-AOM in natural environments is rare, and the mechanisms behind the direct coupling of methane oxidation and iron reduction remain poorly understood. In this study, we investigated the environmental factors influencing the distribution of methanotrophic archaea in an iron-rich zone of a freshwater pond in Hiroshima Prefecture, Japan. High concentration of dissolved ferrous iron supplied by groundwater discharge led to considerable ferrihydrite precipitation. Pore water methane increased with sediment depth, while nitrate and sulfate concentrations were near detection limits throughout the sediment column. The coexistence of ferric iron and methane suggests the ongoing process of Fe-AOM. Tracer-based experiments using 14C showed potential Fe-AOM rates up to 110 pmol mL-1 day-1. Throughout the sediment core, except at the surface, PCR-based molecular ecological analyses of the 16S rRNA gene and functional genes for anaerobic oxidation of methane revealed abundant sequences belonging to the family "Candidatus Methanoperedenaceae". These geochemical and microbiological findings suggest that Fe-AOM plays a key role in biogeochemical cycles of iron and methane, positioning this environment as a modern analogue of early Earth conditions.},
}

*Groundwater/microbiology/chemistry
*Methane/metabolism
*Iron/metabolism
*Archaea/metabolism/genetics
*RNA, Ribosomal, 16S/genetics
*Oxidation-Reduction
Geologic Sediments/microbiology
Phylogeny
Japan
Anaerobiosis

@article {pmid39986474,
year = {2025},
author = {Li, X and Wu, F and Yu, D and Su, X and Wang, K and Huang, Z and Lu, Z},
title = {Archaea-inspired deoxyribonuclease I liposomes prevent multiple organ dysfunction in sepsis.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jconrel.2025.02.050},
pmid = {39986474},
issn = {1873-4995},
abstract = {Neutrophil extracellular traps (NETs) and circulating cell-free DNA (cfDNA) are pivotal in driving excessive inflammation and organ damage during sepsis, with their levels correlating positively with sepsis severity in both patients and murine models. Despite the ability of deoxyribonuclease I (DNase I) to degrade NETs and cfDNA, its short half-life and rapid degradation limit its therapeutic effectiveness. To address this challenge, we developed a methyl-branched liposome fused with a red blood cell membrane for the systemic delivery of DNase I (DNase I/Rm-Lipo). The efficacy of DNase I/Rm-Lipo was evaluated in the stimulated immune cells and septic model. The data confirmed that DNase I/Rm-Lipo efficiently removed excess NETs and cfDNA in activated neutrophils. Following injection, DNase I/Rm-Lipo exhibited an extended circulation time, effectively suppressing neutrophil activation and regulating macrophage polarization to mitigate inflammation and prevent organ dysfunction in septic mice. These findings highlight the therapeutic potential of DNase I/Rm-Lipo as a promising candidate for sepsis management by targeting the degradation of NETs and cfDNA.},
}

@article {pmid39965710,
year = {2025},
author = {Qiu, H and Zhao, W and Qin, Y and Wang, Y and Bai, M and Su, S and Wang, C and Zhao, Z},
title = {Ammonia-oxidizing activity and microbial structure of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and complete ammonia oxidizers in biofilm systems with different salinities.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132248},
doi = {10.1016/j.biortech.2025.132248},
pmid = {39965710},
issn = {1873-2976},
abstract = {Ammonia-oxidizing activity of different ammonia-oxidizing microorganisms (AOMs), such as ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammoxs), were investigated by adding the inhibitors such as 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide, octyne, and KCLO3 in biofilm systems with different salinities. It was found that the ammonia-oxidizing activity of all AOMs gradually decreased with increasing salinity. The ammonia-oxidizing activity of AOB was consistently higher than those of AOA and comammox at different salinities. Moreover, nitrite-oxidizing bacteria (NOB) were more sensitive to changes in salinity than AOMs. Metagenomic analysis revealed that nitrifiers were detected at high level, with the AOB Nitrosomonas sp. comprising 24.9 % and the NOB Nitrospira sp. comprising 47.2 % of all nitrifiers. The main functional genes involved in the nitrification reaction were amoABC, hao, and nxrAB. This study demonstrates that higher abundance of functional microorganisms and genes is related to the ammonia-oxidizing activity and ammonia removal contribution rate.},
}

@article {pmid39919172,
year = {2025},
author = {Souza, DP and Espadas, J and Chaaban, S and Moody, ERR and Hatano, T and Balasubramanian, M and Williams, TA and Roux, A and Baum, B},
title = {Asgard archaea reveal the conserved principles of ESCRT-III membrane remodeling.},
journal = {Science advances},
volume = {11},
number = {6},
pages = {eads5255},
pmid = {39919172},
issn = {2375-2548},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Endosomal Sorting Complexes Required for Transport/metabolism/genetics ; *Archaea/metabolism/genetics ; *Phylogeny ; Cell Membrane/metabolism ; Archaeal Proteins/metabolism/genetics/chemistry ; Evolution, Molecular ; },
abstract = {ESCRT-III proteins assemble into composite polymers that undergo stepwise changes in composition and structure to deform membranes across the tree of life. Here, using a phylogenetic analysis, we demonstrate that the two endosomal sorting complex required for transport III (ESCRT-III) proteins present in eukaryote's closest Asgard archaeal relatives are evolutionarily related to the B- and A-type eukaryotic paralogs that initiate and execute membrane remodeling, respectively. We show that Asgard ESCRT-IIIB assembles into parallel arrays on planar membranes to initiate membrane deformation, from where it recruits ESCRT-IIIA to generate composite polymers. Last, we show that Asgard ESCRT-IIIA is able to remodel membranes into tubes as a likely prelude to scission. Together, these data reveal a set of conserved principles governing ESCRT-III-dependent membrane remodeling that first emerged in a two-component ESCRT-III system in archaea.},
}

*Endosomal Sorting Complexes Required for Transport/metabolism/genetics
*Archaea/metabolism/genetics
*Phylogeny
Cell Membrane/metabolism
Archaeal Proteins/metabolism/genetics/chemistry
Evolution, Molecular

@article {pmid39910065,
year = {2025},
author = {Fumagalli, A and Castells-Nobau, A and Trivedi, D and Garre-Olmo, J and Puig, J and Ramos, R and Ramió-Torrentà, L and Pérez-Brocal, V and Moya, A and Swann, J and Martin-Garcia, E and Maldonado, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2455506},
doi = {10.1080/19490976.2025.2455506},
pmid = {39910065},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; *Butyrates/metabolism ; Humans ; *Cognition ; *Histidine/metabolism ; Male ; Female ; Middle Aged ; Aged ; Bacteria/classification/metabolism/genetics/isolation & purification ; Methanobrevibacter/metabolism/genetics ; Metagenomics ; Archaea/metabolism/classification/genetics ; Cohort Studies ; Animals ; Adult ; },
abstract = {The relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics and neuropsychological tests to identify microbial species associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited the strongest positive associations with cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) of M. smithii (low and high M. smithii groups: LMs and HMs) revealed that HMs exhibited better cognition and distinct gut bacterial profiles (PERMANOVA p = 0.001), characterized by increased levels of Verrucomicrobia, Synergistetes and Lentisphaerae species and reduced levels of Bacteroidetes and Proteobacteria. Several of these species were linked to the cognitive test scores. These findings were replicated in a large-scale validation cohort (Aging Imageomics, n = 942). Functional analyses revealed an enrichment of energy, butyrate, and bile acid metabolism in HMs in both cohorts. Global plasma metabolomics by CIL LC-MS in IRONMET identified an enrichment of methylhistidine, phenylacetate, alpha-linolenic and linoleic acid, and secondary bile acid metabolism associated with increased levels of 3-methylhistidine, phenylacetylgluamine, adrenic acid, and isolithocholic acid in the HMs group. Phenylacetate and linoleic acid metabolism also emerged in the Aging Imageomics cohort performing untargeted HPLC-ESI-MS/MS metabolic profiling, while a targeted bile acid profiling identified again isolithocholic acid as one of the most significant bile acid increased in the HMs. 3-Methylhistidine levels were also associated with intense physical activity in a second validation cohort (IRONMET-CGM, n = 116). Finally, FMT from HMs donors improved cognitive flexibility, reduced weight, and altered SCFAs, histidine-, linoleic acid- and phenylalanine-related metabolites in the dorsal striatum of recipient mice. M. smithii seems to interact with the bacterial ecosystem affecting butyrate, histidine, phenylalanine, and linoleic acid metabolism with a positive impact on cognition, constituting a promising therapeutic target to enhance cognitive performance, especially in subjects with obesity.},
}

*Gastrointestinal Microbiome/physiology
*Butyrates/metabolism
Humans
*Cognition
*Histidine/metabolism
Male
Female
Middle Aged
Aged
Bacteria/classification/metabolism/genetics/isolation & purification
Methanobrevibacter/metabolism/genetics
Metagenomics
Archaea/metabolism/classification/genetics
Cohort Studies
Animals
Adult

@article {pmid39894155,
year = {2025},
author = {Ren, B and Shi, X and Guo, J and Jin, P},
title = {Interaction of sulfate-reducing bacteria and methanogenic archaea in urban sewers, leads to increased risk of proliferation of antibiotic resistance genes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125777},
doi = {10.1016/j.envpol.2025.125777},
pmid = {39894155},
issn = {1873-6424},
abstract = {Sewers are considered a potential reservoir of antibiotic resistance. However, the generation of antibiotic resistance genes (ARGs) in microbial communities in pipeline biofilms under antibiotic stress remains unexplored. In this study, the biodegradation efficiency of tetracycline (TCY) and sulfamethoxazole (SMX) was evaluated in a pilot reactor of the sewers. The results showed that under TCY and SMX stress, the degradation efficiency of sewage water was inhibited. The most abundant ARGs detected in the biofilm samples were TCY-related genes (e.g., tetW/N/W, tetC, and tetM), accounting for 34.1%. The microbial community composition varied, and the correlation analysis showed that antibiotic stress had a certain impact on the biological metabolic activity and function of the urban sewers. The community structure and diversity of biofilms enabled the evaluation of the bioconversion of antibiotics. Notably, Anaerocella and Paludibacter directly influenced the methanogenesis and sulfate reduction processes, playing a key role in the interaction between sulfate-reducing bacteria and methanogenic archaea. These microorganisms facilitated the proliferation of ARGs (tet and sul) in the biofilms through horizontal gene transfer. This study provides insight into the front-end control of ARGs, further improving sewage treatment plant processes and reducing the environmental and health risks caused by antibiotic abuse.},
}

@article {pmid39880954,
year = {2025},
author = {Huang, Y and Igarashi, K and Liu, L and Mayumi, D and Ujiie, T and Fu, L and Yang, M and Lu, Y and Cheng, L and Kato, S and Nobu, MK},
title = {Methanol transfer supports metabolic syntrophy between bacteria and archaea.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39880954},
issn = {1476-4687},
abstract = {In subsurface methanogenic ecosystems, the ubiquity of methylated-compound-using archaea-methylotrophic methanogens[1-4]-implies that methylated compounds have an important role in the ecology and carbon cycling of such habitats. However, the origin of these chemicals remains unclear[5,6] as there are no known energy metabolisms that generate methylated compounds de novo as a major product. Here we identified an energy metabolism in the subsurface-derived thermophilic anaerobe Zhaonella formicivorans[7] that catalyses the conversion of formate to methanol, thereby producing methanol without requiring methylated compounds as an input. Cultivation experiments showed that formate-driven methanologenesis is inhibited by the accumulation of methanol. However, this limitation can be overcome through methanol consumption by a methylotrophic partner methanogen, Methermicoccus shengliensis. This symbiosis represents a fourth mode of mutualistic cross-feeding driven by thermodynamic necessity (syntrophy), previously thought to rely on transfer of hydrogen, formate or electrons[8-10]. The unusual metabolism and syntrophy provide insights into the enigmatic presence of methylated compounds in subsurface methanogenic ecosystems and demonstrate how organisms survive at the thermodynamic limit through metabolic symbiosis.},
}

@article {pmid39869143,
year = {2025},
author = {Zhu, LR and Nwankwo, C and Hou, J and Cui, HL},
title = {Halobellus marinus sp. nov., Halobellus ordinarius sp. nov., Halobaculum rarum sp. nov., and Halorarum halobium sp. nov., halophilic archaea isolated from marine solar salt and a saline lake.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {1},
pages = {13},
pmid = {39869143},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Lakes/microbiology ; *Phylogeny ; Genome, Archaeal ; Seawater/microbiology ; },
abstract = {Four halophilic archaeal strains were isolated from sea salt and a saline lake in China. Based on phylogenetic and phylogenomic analyses, the four strains are related to the genera of Halobellus, Halobaculum, and Halorarum within the family Haloferacaceae. The four strains possess genes responsible for carotenoid synthesis, maintenance of a high internal salt concentration, as well as diverse enzymes with biotechnological potential. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values among these four strains and their related species were lower than the established thresholds proposed for species demarcation. Strains DFY28[T], ZY16[T], QDC11[T], and XH14[T] were distinguished from related species based on a variety of phenotypic characteristics. The major polar lipids of these four strains were similar to those of respective relatives within the genera Halobellus, Halobaculum, and Halorarum. The phenotypic, phylogenetic, and genome-based analyses suggest that strains DFY28[T] (= CGMCC 1.17470[T] = JCM 34310[T]), ZY16[T] (= CGMCC 1.17476[T] = JCM 34311[T]), QDC11[T] (= MCCC 4K00127[T] = KCTC 4308[T]), and XH14[T] (= CGMCC 1.17028[T] = JCM 34145[T]) represent four novel species of the genera Halobellus, Halobaculum and Halorarum, for which the names Halobellus marinus sp. nov., Halobellus ordinarius sp. nov., Halobaculum rarum sp. nov., and Halorarum halobium sp. nov. are proposed.},
}

*Lakes/microbiology
*Phylogeny
Genome, Archaeal
Seawater/microbiology

@article {pmid39863085,
year = {2025},
author = {Yamamura, R and Okubo, R and Ukawa, S and Nakamura, K and Okada, E and Nakagawa, T and Imae, A and Kimura, T and Tamakoshi, A},
title = {Increased fecal glycocholic acid levels correlate with obesity in conjunction with the depletion of archaea: the DOSANCO Health Study.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109846},
doi = {10.1016/j.jnutbio.2025.109846},
pmid = {39863085},
issn = {1873-4847},
abstract = {BACKGROUND: Recent studies have focused on the relationship between obesity and gut microbiota. This study aims to identify fecal components and gut bacterial species associated with different BMI categories.

METHODS: In this study, 538 participants aged ≥18 years were categorized into underweight, normal, and obese groups based on BMI (cutoffs: 18.5 and 25.0 kg/m²). We compared 30 fecal components among these groups and calculated correlation coefficients between each component and BMI. Participants were then divided into quartiles based on fecal component levels correlated with BMI, and the prevalence ratio (PR) of obesity was calculated, adjusted for confounding factors. We also analyzed the composition and diversity of gut microbiota and bacterial gene expression among the quartiles for each fecal component.

RESULTS: Fecal glycocholic acid (GCA) showed a significant positive correlation with BMI. The PR for obesity in the highest quartile of fecal GCA was 3.30 (95% CI: 1.21-9.54), indicating a significantly higher risk of obesity compared to the lowest quartile. Gut microbiota analysis revealed significant differences in the abundance of Ruminococcaceae Incertae Sedis, Faecalibacterium, and Methanobrevibacter, with Methanobrevibacter being absent in the higher quartiles of fecal GCA. Additionally, gene expression for enzymes involved in the deconjugation of conjugated bile acids, including GCA, was downregulated in the highest quartile.

CONCLUSIONS: Increased fecal GCA levels are positively correlated with obesity, alongside a depletion of archaea.},
}

@article {pmid39858853,
year = {2025},
author = {Salas-López, M and Vélez-Ixta, JM and Rojas-Guerrero, DL and Piña-Escobedo, A and Hernández-Hernández, JM and Rangel-Calvillo, MN and Pérez-Cruz, C and Corona-Cervantes, K and Juárez-Castelán, CJ and García-Mena, J},
title = {Human Milk Archaea Associated with Neonatal Gut Colonization and Its Co-Occurrence with Bacteria.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/microorganisms13010085},
pmid = {39858853},
issn = {2076-2607},
support = {CONACYT-163235, INFR-2011-01.//Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT) Mexico/ ; CONACYT FORDECYT-PRONACES/6669/2020_Programa Presupuestario F003-Ciencia de Frontera 2019.//Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT) Mexico/ ; },
abstract = {Archaea have been identified as early colonizers of the human intestine, appearing from the first days of life. It is hypothesized that the origin of many of these archaea is through vertical transmission during breastfeeding. In this study, we aimed to characterize the archaeal composition in samples of mother-neonate pairs to observe the potential vertical transmission. We performed a cross-sectional study characterizing the archaeal diversity of 40 human colostrum-neonatal stool samples by next-generation sequencing of V5-V6 16S rDNA libraries. Intra- and inter-sample analyses were carried out to describe the Archaeal diversity in each sample type. Human colostrum and neonatal stools presented similar core microbiota, mainly composed of the methanogens Methanoculleus and Methanosarcina. Beta diversity and metabolic prediction results suggest homogeneity between sample types. Further, the co-occurrence network analysis showed associations between Archaea and Bacteria, which might be relevant for these organisms' presence in the human milk and neonatal stool ecosystems. According to relative abundance proportions, beta diversity, and co-occurrence analyses, the similarities found imply that there is vertical transmission of archaea through breastfeeding. Nonetheless, differential abundances between the sample types suggest other relevant sources for colonizing archaea to the neonatal gut.},
}

@article {pmid39857234,
year = {2024},
author = {Yoshimura, A and Seki, M},
title = {The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements.},
journal = {Biology},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/biology14010003},
pmid = {39857234},
issn = {2079-7737},
abstract = {We propose a hypothesis for the simultaneous emergence of bacteria, archaea, viruses, and mobile elements by sequential and concrete biochemical pathways. The emergence process can be considered analogous to crystallization, where genetic and biochemical systems stabilize as organisms evolve from their common ancestor, the LUCA, which was a non-free-living pool of single operon type genomes including double-stranded (ds) DNA at an ancient submarine alkaline vent. Each dsDNA operon was transcribed by different systems in σ, TFIIB, or TBP genomes. Double-stranded DNA operons can fuse and stabilize through the action of specific transcription systems, leading to differentiation between the Bacteria (σ genome) and Archaea (TBP genome) domains. Error catastrophe can be overcome by the parallel gain of DNA replication and DNA repair mechanisms in both genomes. Enlarged DNA enabled efficient local biochemical reactions. Both genomes independently recruited lipids to facilitate reactions by forming coacervates at the chamber of the vent. Bilayer lipid membrane formation, proto-cell formation with a permeable membrane, proto-cell division, and the evolution of membrane-associated biochemistry are presented in detail. Simultaneous crystallization of systems in non-free-living bacteria and non-free-living archaea triggered the co-crystallization of primitive viruses and mobile elements. An arms race between non-free-living cells and primitive viruses finally led to free-living cells with a cell wall and mature viruses.},
}

@article {pmid39856443,
year = {2025},
author = {Song, N and Li, M},
title = {Convergent and conserved roads lead to Rome: now archaea fill the gap of transcription termination.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {39856443},
issn = {1869-1889},
}

@article {pmid39848515,
year = {2025},
author = {Zhang, M and Bai, L and Yao, Z and Li, W and Yang, W},
title = {Seasonal Lake Ice Cover Drives the Restructuring of Bacteria-Archaea and Bacteria-Fungi Interdomain Ecological Networks Across Diverse Habitats.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120907},
doi = {10.1016/j.envres.2025.120907},
pmid = {39848515},
issn = {1096-0953},
abstract = {The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.},
}

@article {pmid39845047,
year = {2024},
author = {Gfellner, SV and Colas, C and Gabant, G and Groninga, J and Cadene, M and Milojevic, T},
title = {Improved protocol for metabolite extraction and identification of respiratory quinones in extremophilic Archaea grown on mineral materials.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1473270},
pmid = {39845047},
issn = {1664-302X},
abstract = {We investigated the metabolome of the iron- and sulfur-oxidizing, extremely thermoacidophilic archaeon Metallosphaera sedula grown on mineral pyrite (FeS2). The extraction of organic materials from these microorganisms is a major challenge because of the tight contact and interaction between cells and mineral materials. Therefore, we applied an improved protocol to break the microbial cells and separate their organic constituents from the mineral surface, to extract lipophilic compounds through liquid-liquid extraction, and performed metabolomics analyses using MALDI-TOF MS and UHPLC-UHR-Q/TOF. Using this approach, we identified several molecules involved in central carbon metabolism and in the modified Entner-Doudoroff pathway found in Archaea, sulfur metabolism-related compounds, and molecules involved in the adaptation of M. sedula to extreme environments, such as metal tolerance and acid resistance. Furthermore, we identified molecules involved in microbial interactions, i.e., cell surface interactions through biofilm formation and cell-cell interactions through quorum sensing, which relies on messenger molecules for microbial communication. Moreover, we successfully extracted and identified different saturated thiophene-bearing quinones using software for advanced compound identification (MetaboScape). These quinones are respiratory chain electron carriers in M. sedula, with biomarker potential for life detection in extreme environmental conditions.},
}

@article {pmid39824485,
year = {2025},
author = {McAllister, TA and Thomas, KD and Gruninger, RJ and Elshahed, M and Li, Y and Cheng, Y},
title = {INTERNATIONAL SYMPOSIUM ON RUMINANT PHYSIOLOGY: Rumen fungi, archaea and their interactions.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25713},
pmid = {39824485},
issn = {1525-3198},
abstract = {Anaerobic gut fungi (AGF) were the last phylum to be identified within the rumen microbiome and account for 7-9% of microbial biomass. They produce potent lignocellulases that degrade recalcitrant plant cell walls, and rhizoids that can penetrate the cuticle of plant cells, exposing internal components to other microbiota. Interspecies H2 transfer between AGF and rumen methanogenic archaea is an essential metabolic process in the rumen that occurs during the reduction of CO2 to CH4 by methanogens. This symbiotic relationship is bolstered by hydrogensomes, fungal organelles that generate H2 and formate. Interspecies H2 transfer prevents the accumulation of reducing equivalents that would otherwise impede fermentation. The extent to which hydrogenosomes serve as a conduit for H2 flow to methanogens is unknown, but it is likely greater with low quality forages. Strategies that alter the production of CH4 could also have implications for H2 transfer by anaerobic fungi. Understanding the factors that drive these interactions and H2 flow could provide insight into the effect of reducing CH4 production on the activity of ruminal fungi and the digestion of low-quality feeds.},
}

@article {pmid39791890,
year = {2025},
author = {Soborowski, AL and Hackley, RK and Hwang, S and Zhou, G and Dulmage, KA and Schönheit, P and Daniels, C and Bisson-Filho, AW and Marchfelder, A and Maupin-Furlow, JA and Allers, T and Schmid, AK},
title = {Genomic re-sequencing reveals mutational divergence across genetically engineered strains of model archaea.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0108424},
doi = {10.1128/msystems.01084-24},
pmid = {39791890},
issn = {2379-5077},
abstract = {UNLABELLED: Archaeal molecular biology has been a topic of intense research in recent decades as their role in global ecosystems, nutrient cycles, and eukaryotic evolution comes to light. The hypersaline-adapted archaeal species Halobacterium salinarum and Haloferax volcanii serve as important model organisms for understanding archaeal genomics, genetics, and biochemistry, in part because efficient tools enable genetic manipulation. As a result, the number of strains in circulation among the haloarchaeal research community has increased in recent decades. However, the degree of genetic divergence and effects on genetic integrity resulting from the creation and inter-lab transfer of novel lab stock strains remain unclear. To address this, we performed whole-genome re-sequencing on a cross-section of wild-type, parental, and knockout strains in both model species. Integrating these data with existing repositories of re-sequencing data, we identify mutations that have arisen in a collection of 60 strains, sampled from two species across eight different labs. Independent of sequencing, we construct strain lineages, identifying branch points and significant genetic events in strain history. Combining this with our sequencing data, we identify small clusters of mutations that definitively separate lab strains. Additionally, an analysis of gene knockout strains suggests that roughly one in three strains currently in use harbors second-site mutations of potential phenotypic impact. Overall, we find that divergence among lab strains is thus far minimal, though as the archaeal research community continues to grow, careful strain provenance and genomic re-sequencing are required to keep inter-lab divergence to a minimum, prevent the compounding of mutations into fully independent lineages, and maintain the current high degree of reproducible research between lab groups.

IMPORTANCE: Archaea are a domain of microbial life whose member species play a critical role in the global carbon cycle, climate regulation, the human microbiome, and persistence in extreme habitats. In particular, hypersaline-adapted archaea are important, genetically tractable model organisms for studying archaeal genetics, genomics, and biochemistry. As the archaeal research community grows, keeping track of the genetic integrity of strains of interest is necessary. In particular, routine genetic manipulations and the common practice of sharing strains between labs allow mutations to arise in lab stocks. If these mutations affect cellular processes, they may jeopardize the reproducibility of work between research groups and confound the results of future studies. In this work, we examine DNA sequences from 60 strains across two species of archaea. We identify shared and unique mutations occurring between and within strains. Independently, we trace the lineage of each strain, identifying which genetic manipulations lead to observed off-target mutations. While overall divergence across labs is minimal so far, our work highlights the need for labs to continue proper strain husbandry.},
}

@article {pmid39777146,
year = {2024},
author = {Unis, R and Gnaim, R and Kashyap, M and Shamis, O and Gnayem, N and Gozin, M and Liberzon, A and Gnaim, J and Golberg, A},
title = {Bioconversion of bread waste into high-quality proteins and biopolymers by fermentation of archaea Haloferax mediterranei.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1491333},
pmid = {39777146},
issn = {1664-302X},
abstract = {The valorization of bread waste into high-quality protein and biopolymers using the halophilic microorganism Haloferax mediterranei presents a sustainable approach to food waste management and resource optimization. This study successfully coproduced protein and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) biopolymer with a biomass content of 8.0 ± 0.1 g L[-1] and a productivity of 11.1 mg L[-1] h[-1]. The fermentation process employed 3.0% w/v of enzymatically hydrolyzed bread waste. The amino acid profile of the cell biomass revealed a total content of 358 g kg[-1] of biomass dry weight (DW), including 147 g kg[-1] DW of essential amino acids. The protein quality, assessed through in-vitro enzyme digestion, indicated a high-quality protein with a digestibility value of 0.91 and a protein digestibility-corrected amino acid score (PDCAAS) of 0.78. The PHBV biopolymer component (36.0 ± 6.3% w/w) consisted of a copolymer of 3-hydroxybutyrate and 3-hydroxyvalerate in a 91:9 mol% ratio. This bioconversion process not only mitigates food waste but also generates valuable biomaterials.},
}

@article {pmid39774673,
year = {2025},
author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F},
title = {Author Correction: Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {453},
doi = {10.1038/s41467-024-55458-6},
pmid = {39774673},
issn = {2041-1723},
}

@article {pmid39756384,
year = {2025},
author = {Ma, X and Lv, J and Ma, X and Zhu, D and Long, Q and Xing, J},
title = {Isolation optimization and screening of halophilic enzymes and antimicrobial activities of halophilic archaea from the high-altitude, hypersaline Da Qaidam Salt lake, China.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf002},
pmid = {39756384},
issn = {1365-2672},
abstract = {AIM: The aim of this study is to increase the diversity of culturable halophilic archaea by comparing various isolation conditions and to explore the application of halophilic archaea for enzyme-producing activities and antimicrobial properties.

METHODS AND RESULTS: We systematically compared the isolation performance of various archaeal and bacterial media by isolating halophilic archaea from the Da Qaidam Salt Lake, a magnesium sulfate subtype hypersaline lake on the Qinghai-Tibet Plateau, China, using multiple enrichment culture and gradient dilution conditions. A total of 490 strains of halophilic archaea were isolated, which belonged to five families and 11 genera within the order Halobacteriales of the class Halobacteria of the phylum Euryarchaeota. The 11 genera consisted of nine known genera and two potentially new genera, the former including Halorubrum, Natranaeroarchaeum, Haloplanus, Haloarcula, Halorhabdus, Halomicrobium, Halobacterium, Natrinema and Haloterrigene. Halorubrum was the dominant genus with a relative abundance of 78.98%. By comparing different culture conditions, we found that bacterial media 2216E and R2A showed much better isolation performance than all archaeal media, and enrichment culture after 60 days and dilution gradients of 10-1 and 10-2 were best fitted for halophilic archaea cultivation. The screening of 40 halophilic archaeal strains of different species indicated that these halophilic archaea had great extracellular enzyme activities including amylase (62.5%), esterase (50.0%), protease (27.5%) and cellulase (15.0%), and possessed great antimicrobial activities against human pathogens. 34 strains exhibited antimicrobial activity against four or more pathogens, and 19 strains exhibited antimicrobial activity against all six pathogens.

CONCLUSIONS: The diversity of culturable halophilic archaea was significantly increased by enrichment culture and selection of bacterial media, and screening of representative strains showed that halophilic archaea have multiple extracellular enzyme activities and broad-spectrum antimicrobial activity against human pathogens.},
}

@article {pmid39709598,
year = {2024},
author = {Villain, P and Basta, T},
title = {Regulation of DNA Topology in Archaea: State of the Art and Perspectives.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.15328},
pmid = {39709598},
issn = {1365-2958},
support = {//Centre National de la Recherche Scientifique/ ; },
abstract = {DNA topology is a direct consequence of the double helical nature of DNA and is defined by how the two complementary DNA strands are intertwined. Virtually every reaction involving DNA is influenced by DNA topology or has topological effects. It is therefore of fundamental importance to understand how this phenomenon is controlled in living cells. DNA topoisomerases are the key actors dedicated to the regulation of DNA topology in cells from all domains of life. While significant progress has been made in the last two decades in understanding how these enzymes operate in vivo in Bacteria and Eukaryotes, studies in Archaea have been lagging behind. This review article aims to summarize what is currently known about DNA topology regulation by DNA topoisomerases in main archaeal model organisms. These model archaea exhibit markedly different lifestyles, genome organization and topoisomerase content, thus highlighting the diversity and the complexity of DNA topology regulation mechanisms and their evolution in this domain of life. The recent development of functional genomic assays supported by next-generation sequencing now allows to delve deeper into this timely and exciting, yet still understudied topic.},
}

@article {pmid39700724,
year = {2024},
author = {Mao, YL and Dong, XY and Tao, CQ and Wu, ZP and Shi, XW and Hou, J and Cui, HL},
title = {Natronorarus salvus gen. nov., sp. nov., Halalkalicoccus ordinarius sp. nov., and Halalkalicoccus salilacus sp. nov., halophilic archaea from a soda lake and two saline lakes, and proposal to classify the genera Halalkalicoccus and Natronorarus into Halalkalicoccaceae fam. nov. in the order Halobacteriales within the class Halobacteria.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {1},
pages = {126577},
doi = {10.1016/j.syapm.2024.126577},
pmid = {39700724},
issn = {1618-0984},
abstract = {Four novel halophilic archaeal strains CGA53[T], CG83[T], FCH27[T], and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53[T] showed the highest 16S rRNA gene similarity (92.6%) to Salinilacihabitans rarus AD-4[T], and the other three strains were found to be related to Halalkalicoccus species with similarities of 97.6-98.3%. Metagenomic studies indicated that these four strains are low abundant inhabitants detected in these hypersaline environments, and only one MAG of Chagannuoer Soda Lake (CG) could be assigned to the genus Halalkalicoccus. Their growth occurred at 20-60 °C (optima, 42, 37, 37-42, and 35 °C), 0.9-5.1 M NaCl (optima, 3.9, 2.6, 3.5, and 3 M), and 0-1.0 M MgCl2 (optima, 0.5, 0.7, and 0.1) and pH 5.5-10.5 (optima, 9.0, 7.5, 7.0, and 7.0), respectively. Phylogenetic and phylogenomic analyses revealed that strains CG83[T], FCH27[T], and SEDH24 cluster with the current species of the genus Halalkalicoccus, and strain CGA53[T] forms an independent branch separated from this genus. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among strains CGA53[T], CG83[T], FCH27[T], SEDH24, and the type species of the current genera within the class Halobacteria were 67.4-81.6%, 16.5-28.6% and 49.7-74.1%, respectively, clearly lower than the cutoff values for species demarcation. Strain CGA53[T] may represent a novel species of a new genus according to the cutoff value for genus demarcation of 65% AAI. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, antibiotic sensitivity, and H2S formation, were found among these four strains and Halalkalicoccus species. Genome-based classification supported that strains CGA53[T], CG83[T], FCH27[T], SEDH24, and the current species of Halalkalicoccus represent a novel family of the order Halobacteriales within the class Halobacteria.},
}

@article {pmid39699520,
year = {2024},
author = {Vargas, LC and Faria, LC and Pereira, LT and Signori, CN},
title = {Water masses drive the spatial and temporal distribution of marine Archaea in the northern Antarctic Peninsula.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {96},
number = {suppl 2},
pages = {e20240585},
doi = {10.1590/0001-3765202420240585},
pmid = {39699520},
issn = {1678-2690},
mesh = {Antarctic Regions ; *Archaea/classification/genetics/isolation & purification ; *Seawater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Seasons ; Spatio-Temporal Analysis ; },
abstract = {The Southern Ocean influences the planet's biogeochemical cycles. Marine microorganisms are important in this scenario, being the main biological agents in the cycling of many elements. The Archaea domain is widely distributed in the oceans, and its presence in Antarctica is acknowledged. In this context, this work aimed to analyze the diversity and distribution of archaea according to environmental parameters in the waters surrounding the north of the Antarctic Peninsula. For environmental characterization studies, surface and bottom data were used for the ten monitoring stations of expeditions that took place in the summer of 2014 and 2015. The sequencing of the 16S rRNA gene was performed on the Illumina HiSeq platform, using the SILVA v138 database. The results revealed the presence of three main water bodies: Antarctic Surface Water, Shelf Waters, and modified Circumpolar Deep Water. Deep waters had higher diversity than surface waters, and the dominant groups were Nitrososphaeria and MGII. In the study region, the main factor responsible for the differences in the ecosystems was the presence of distinct water masses and the stratification of the water column. We argue that it is essential to consider water mass dynamics to study the microbial landscape of the Southern Ocean.},
}

Antarctic Regions
*Archaea/classification/genetics/isolation & purification
*Seawater/microbiology
*RNA, Ribosomal, 16S/genetics
*Biodiversity
Seasons
Spatio-Temporal Analysis

@article {pmid39688758,
year = {2024},
author = {Řezanka, P and Řezanka, M and Kyselová, L and Řezanka, T},
title = {Characterization of Archaea membrane lipids in radioactive springs using shotgun lipidomics.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39688758},
issn = {1874-9356},
support = {MZE-RO1923//Ministerstvo Zemědělství/ ; RVO61388971//Mikrobiologický Ústav, Akademie Věd České Republiky/ ; },
abstract = {Lipids from microorganisms, and especially lipids from Archaea, are used as taxonomic markers. Unfortunately, knowledge is very limited due to the uncultivability of most Archaea, which greatly reduces the importance of the diversity of lipids and their ecological role. One possible solution is to use lipidomic analysis. Six radioactive sources were investigated, two of which are surface (Wettinquelle and Radonka) and four deep from the Svornost mine (Agricola, Behounek, C1, and Curie). A total of 15 core lipids and 82 intact polar lipids were identified from the membranes of microorganisms in six radioactive springs. Using shotgun lipidomics, typical Archaea lipids were identified in spring water, namely dialkyl glycerol tetraethers, archaeol, hydroxyarchaeol and dihydroxyarchaeol. Diverse groups of polar heads were formed in archaeal IPLs, whose polar heads are formed mainly by hexose, deoxyhexose, and phosphoglycerol. The analysis was performed using shotgun lipidomics and the structure of all molecular species was confirmed by tandem mass spectrometry. After acid hydrolysis, a mixture of polar compounds was obtained from the polar head. Further analysis by GC-MS confirmed that the carbohydrates were glucose and rhamnose. Analysis by HPLC-MS of diastereoisomers of 2-(polyhydroxyalkyl)-3-(O-tolylthiocarbamoyl)thiazolidine-4(R)-carboxylates revealed that both L-rhamnose and D-glucose are present in spring samples only in varying amounts. The glycoside composition depends on the type of spring, that is, Wettinquelle and Radonka springs are basically shallow groundwater, while the samples from the Svornost mine are deep groundwater and do not contain glycosides with rhamnose. This method enables quick screening for characteristic Archaea lipids, allowing decisions on whether to pursue further analyses, such as metagenomic analysis, to directly confirm the presence of Archaea.},
}

@article {pmid39682435,
year = {2024},
author = {Dou, X and Zhang, G and Tang, H and Chen, X and Chen, B and Mei, Y and Jiao, H and Ren, M},
title = {Carotenoids from Halophilic Archaea: A Novel Approach to Improve Egg Quality and Cecal Microbiota in Laying Hens.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/ani14233470},
pmid = {39682435},
issn = {2076-2615},
support = {TDZKCX202413//the President's Fund of Tarim University/ ; 31900007//the National Natural Science Foundation of China/ ; 202410757009//Innovation and Entrepreneurship Training Program for College Students of Tarim University/ ; },
abstract = {Carotenoids from different sources have different structures and functions, and their dietary components benefit the health of various organisms. The effects of halophilic Archaea-derived C50 carotenoids on poultry egg quality and gut microbiota remain largely unexplored. In this study, we isolated a carotenoid-secreting strain of Halalkalicoccus paucihalophilus, TRM89021, from the Pamir Plateau. We characterized the carotenoid pigments produced by this strain; the major components were bacterioruberin and its derivatives. The effects of these carotenoids on the egg quality and cecal microbiota composition of hens were investigated. Compared to the basal diet group (BDG), supplementation with carotenoids in the carotenoids-supplemented diet group (CDG) resulted in significantly lower a* and b* scores at week 5 and lower b* scores and Haugh units at week 2, while egg strength and weight were higher. CDG also showed increased yolk antioxidant capacity, higher glutathione peroxidase levels, and significantly lower catalase levels (p < 0.05). Plasma analysis revealed elevated total bilirubin and aspartate aminotransferase levels, along with reduced inorganic phosphorus levels in the CDG (p < 0.05). No significant differences in cecal microbiota diversity were observed between the groups at any taxonomic level. This result suggests that halophilic archaea-derived carotenoids have the potential to be used as natural feed supplements to improve egg quality. Our study provides a theoretical basis for applying archaea-derived carotenoids in poultry diets.},
}

@article {pmid39663550,
year = {2024},
author = {Saranya, S and Prathiviraj, R and Chellapandi, P},
title = {Evolutionary Transitions of DNA Replication Origins Between Archaea and Bacteria.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e2400527},
doi = {10.1002/jobm.202400527},
pmid = {39663550},
issn = {1521-4028},
support = {//This work was funded by Science and Engineering Research Board, Ministry of Science and Technology, Government of India, Grant/Award Number EEQ/2020/000095 and Ministry of Education, India, Rashtriya Uchchatar Shiksha Abhiyan, Grant/Award Number 12/BDU/RUSA/TRP/BS./ ; },
abstract = {DNA replication origins play a crucial role in cellular division and are evolutionarily conserved across domains. This study investigated the evolutionary transitions of replication origins between archaea and bacteria by analyzing 2733 bacterial and 257 archaeal genomes. Our findings revealed that certain methanogens and bacteria share phylogenetic proximity, suggesting evolutionary interactions across diverse ecological systems. Evolutionary transitions in replication origins may have occurred between gut methanogens and bacteria, haloarchaea (Halogeometricum borinquense DSM 11551 and Halovivax ruber XH-70), halobacteria, and sulfur-reducing archaea. Methanosarcina barkeri (M. barkeri), Methanosaeta thermophila, and Methanococcoides burtonii (M. burtonii) were closely related to respiratory tract bacteria in humans. Methanohalobium evestigatum (M. evestigatum) is strongly linked to the animal gut pathogen Mycoplasma putrefaciens (M. putrefaciens). Several thermophilic hydrogenotrophic methanogens clustered with oral and fish pathogens. Pyrococcus furiosus (P. furiosus) was evolutionarily related to the replication origin of plant pathogens. This study sheds light on the ecological drivers of DNA replication origin evolution and their role in microbial speciation and adaptation. Our findings highlight the influence of mutualistic and parasitic relationships on these evolutionary transitions. It could have significant implications in biotechnology and medicine, such as developing novel antimicrobial strategies and understanding host-pathogen dynamics.},
}

@article {pmid39657077,
year = {2024},
author = {Najjari, A and Elmnasri, K and Cherif, H and Burleigh, S and Guesmi, A and Mahjoubi, M and Linares-Pastén, JA and Cherif, A and Ouzari, HI},
title = {Metataxonomic analysis of halophilic archaea community in two geothermal oases in the southern Tunisian Sahara.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae106},
pmid = {39657077},
issn = {1574-6968},
abstract = {This study assesses halophilic archaea's phylogenetic diversity in southern Tunisia's geothermal water. In the arid southern regions, limited surface freshwater resources make geothermal waters a vital source for oases and greenhouse irrigation. Three samples, including water, sediment, and halite-soil crust, were collected downstream of two geothermal springs of the Ksar Ghilane (KGH) and Zaouet Al Aness (ZAN) oases, Tunisia. The samples were subjected to 16S rRNA gene sequencing using the Illumina Miseq sequencing approach. Several haloarchaea were identified in the geothermal springs. The average taxonomic composition revealed that 20 out of 33 genera were shared between the two geothermal sources, with uneven distribution, where the Halogranum genus was the most represented genus with an abundance of 18.9% and 11.58% for ZAW and KGH, respectively. Several unique site-specific genera were observed: Halonotius, Halopelagius, Natronorubrum, and Haloarcula in ZAN, and Haloprofundus, Halomarina, Halovivax, Haloplanus, Natrinema, Halobium, Natronoarchaeum, and Haloterrigena in the KGH pool. Most genus members are typically found in low-salinity ecosystems. These findings suggest that haloarchaea can disperse downstream from geothermal sources and may survive temperature and chemical fluctuations in the runoff.},
}

@article {pmid39611976,
year = {2024},
author = {Riyaz, Z and Khan, ST},
title = {Nitrogen fixation by methanogenic Archaea, literature review and DNA database-based analysis; significance in face of climate change.},
journal = {Archives of microbiology},
volume = {207},
number = {1},
pages = {6},
pmid = {39611976},
issn = {1432-072X},
mesh = {*Nitrogen Fixation/genetics ; *Archaea/genetics/metabolism/classification ; *Climate Change ; *Soil Microbiology ; Phylogeny ; Databases, Nucleic Acid ; Methane/metabolism ; DNA, Archaeal/genetics ; },
abstract = {Archaea represents a significant population of up to 10% in soil microbial communities. The role of Archaea in soil is often overlooked mainly due to its unculturability. Among the three domains of life biological nitrogen fixation (BNF) is mainly a trait of Eubacteria and some Archaea. Archaea mediated processes like BNF may become even more important in the face of global Climate change. Although there are reports on nitrogen fixation by Archaea, to best of our knowledge there is no comprehensive report on BNF by Archaea under environmental stresses typical to climate change. Here we report a survey of literature and DNA database to study N2-fixation among Archaea. A total of 37 Archaea belonging to Methanogens of the phylum Euryarchaeota within the class Methanococcus, Methanomicrobia Methanobacteria, and Methanotrophic ANME2 lineages either contain genes for BNF or are known to fix atmospheric N2. Archaea were found to have their nif genes arranged as clusters of 6-8 genes in a single operon. The genes code for commonly found Mo-nitrogenase while in some archaea the genes for alternative metal nitrogenases like vnf were also found. The nifHDK gene similarity matrices show that Archaea shared the highest similarity with the nifHDK gene of anaerobic Clostridium beijerinckii. Although there are various theories about the origin of N2-fixation in Archaea, the most acceptable is the origin of N2-fixation first in bacteria and its subsequent transfer to Archaea. Since Archaea can survive under extreme environmental conditions their role in BNF should be studied especially in soil under environmental stress.},
}

*Nitrogen Fixation/genetics
*Archaea/genetics/metabolism/classification
*Climate Change
*Soil Microbiology
Phylogeny
Databases, Nucleic Acid
Methane/metabolism
DNA, Archaeal/genetics

@article {pmid39604363,
year = {2024},
author = {Ma, J and Yi, G and Ye, M and MacGregor-Chatwin, C and Sheng, Y and Lu, Y and Li, M and Li, Q and Wang, D and Gilbert, RJC and Zhang, P},
title = {Open architecture of archaea MCM and dsDNA complexes resolved using monodispersed streptavidin affinity CryoEM.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10304},
pmid = {39604363},
issn = {2041-1723},
support = {206422/Z/17/Z//Wellcome Trust (Wellcome)/ ; BB/S003339/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 101021133//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; U54 AI170791-7522//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21 CA280467/CA/NCI NIH HHS/United States ; },
mesh = {*Cryoelectron Microscopy/methods ; *Streptavidin/chemistry/metabolism ; *Thermococcus/metabolism ; Archaeal Proteins/metabolism/chemistry/ultrastructure ; DNA/metabolism/chemistry ; Minichromosome Maintenance Proteins/metabolism/chemistry ; Biotinylation ; Models, Molecular ; DNA, Archaeal/metabolism/genetics/chemistry ; Saccharomyces cerevisiae/metabolism ; Adenosine Triphosphate/metabolism/chemistry ; },
abstract = {The cryo-electron microscopy (cryoEM) method has enabled high-resolution structure determination of numerous biomolecules and complexes. Nevertheless, cryoEM sample preparation of challenging proteins and complexes, especially those with low abundance or with preferential orientation, remains a major hurdle. We developed an affinity-grid method employing monodispersed single particle streptavidin on a lipid monolayer to enhance particle absorption on the grid surface and alleviate sample exposure to the air-water interface. Using this approach, we successfully enriched the Thermococcus kodakarensis mini-chromosome maintenance complex 3 (MCM3) on cryoEM grids through biotinylation and resolved its structure. We further utilized this affinity method to tether the biotin-tagged dsDNA to selectively enrich a stable MCM3-ATP-dsDNA complex for cryoEM structure determination. Intriguingly, both MCM3 apo and dsDNA bound structures exhibit left-handed open spiral conformations, distinct from other reported MCM structures. The large open gate is sufficient to accommodate a dsDNA which could potentially be melted. The value of mspSA affinity method was further demonstrated by mitigating the issue of preferential angular distribution of HIV-1 capsid protein hexamer and RNA polymerase II elongation complex from Saccharomyces cerevisiae.},
}

*Cryoelectron Microscopy/methods
*Streptavidin/chemistry/metabolism
*Thermococcus/metabolism
Archaeal Proteins/metabolism/chemistry/ultrastructure
DNA/metabolism/chemistry
Minichromosome Maintenance Proteins/metabolism/chemistry
Biotinylation
Models, Molecular
DNA, Archaeal/metabolism/genetics/chemistry
Saccharomyces cerevisiae/metabolism
Adenosine Triphosphate/metabolism/chemistry

@article {pmid39577734,
year = {2024},
author = {Di Giulio, M},
title = {The existence of the two domains of life, Bacteria and Archaea, would in itself imply that LUCA and the ancestors of these domains were progenotes.},
journal = {Bio Systems},
volume = {247},
number = {},
pages = {105375},
doi = {10.1016/j.biosystems.2024.105375},
pmid = {39577734},
issn = {1872-8324},
abstract = {The length of the deepest branches of the tree of life would tend to support the hypothesis that the distance of the branch that separates the sequences of archaea from those of bacteria, i.e. the interdomain one, is longer than the intradomain ones, i.e. those that separate the sequences of archaea and those of bacteria within them. Why should interdomain distance be larger than intradomain distances? The fact that the rate of amino acid substitutions was slowed as the domains of life appeared would seem to imply an evolutionary transition. The slowdown in the speed of evolution that occurred during the formation of the two domains of life would be the consequence of the progenote- > cell evolutionary transition. Indeed, the evolutionary stage of the progenote being characterized by an accelerated tempo and mode of evolution might explain the considerable interdomain distance because the accumulation of many amino acid substitutions on this branch would indicate the progenote stage that is also characterized by a high rate of amino acid substitutions. Furthermore, the fact that intradomain distances are smaller than interdomain distances would corroborate the hypothesis of the achievement of cellularity at the appearance of the main phyletic lineages. Indeed, the cell stage, unlike the progenotic one, definitively establishes the relationship between the genotype and phenotype, lowering the rate of evolution. Therefore, the arguments presented lead to the conclusion that LUCA was a progenote.},
}

@article {pmid39572458,
year = {2024},
author = {Tamang, M and Sikorski, J and van Bommel, M and Piecha, M and Urich, T and Ruess, L and Huber, K and Neumann-Schaal, M and Pester, M},
title = {Succession of Bacteria and Archaea Within the Soil Micro-Food Web Shifts Soil Respiration Dynamics.},
journal = {Environmental microbiology},
volume = {26},
number = {11},
pages = {e70007},
pmid = {39572458},
issn = {1462-2920},
support = {HU3067/1-1//German Research Foundation (SPP 2322)/ ; NE2192/4-1//German Research Foundation (SPP 2322)/ ; PE2147/6-1//German Research Foundation (SPP 2322)/ ; RU 780/22-1//German Research Foundation (SPP 2322)/ ; UR198/7-1//German Research Foundation (SPP 2322)/ ; },
mesh = {*Soil Microbiology ; *Archaea/genetics/classification ; *Bacteria/classification/genetics ; *Soil/chemistry ; *Food Chain ; *Microbiota ; Animals ; *Zea mays/microbiology ; *RNA, Ribosomal, 16S/genetics ; Nematoda/microbiology ; },
abstract = {Bacterivorous nematodes are important grazers in the soil micro-food web. Their trophic regulation shapes the composition and ecosystem services of the soil microbiome, but the underlying population dynamics of bacteria and archaea are poorly understood. We followed soil respiration and 221 dominant bacterial and archaeal 16S rRNA gene amplicon sequencing variants (ASVs) in response to top-down control by a common bacterivorous soil nematode, Acrobeloides buetschlii, bottom-up control by maize litter amendment and their combination over 32 days. Maize litter amendment significantly increased soil respiration, while A. buetschlii addition caused an earlier peak in soil respiration. Underlying bacterial and archaeal population dynamics separated into five major response types, differentiating in their temporal abundance maxima and minima. In-depth analysis of these population dynamics identified a broad imprint of A. buetschlii grazing on dominant bacterial (Acidobacteriota, Bacteroidota, Gemmatimonadota, Pseudomonadota) and archaeal (Nitrososphaerota) ASVs. Combined bottom-up control by maize litter and top-down control by A. buetschlii grazing caused a succession of soil microbiota, driven by population changes first in the Bacteroidota, then in the Pseudomonadota and finally in the Acidobacteriota and Nitrososphaerota. Our results are an essential step forward in understanding trophic modulation of soil microbiota and its feedback on soil respiration.},
}

*Soil Microbiology
*Archaea/genetics/classification
*Bacteria/classification/genetics
*Soil/chemistry
*Food Chain
*Microbiota
Animals
*Zea mays/microbiology
*RNA, Ribosomal, 16S/genetics
Nematoda/microbiology

@article {pmid39568122,
year = {2024},
author = {Matarredona, L and Zafrilla, B and Camacho, M and Bonete, MJ and Esclapez, J},
title = {Understanding the tolerance of halophilic archaea to stress landscapes.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70039},
doi = {10.1111/1758-2229.70039},
pmid = {39568122},
issn = {1758-2229},
support = {VIGROB-016//Universidad de Alicante/ ; CIAICO/2022/047//Generalitat Valenciana/ ; },
mesh = {*Stress, Physiological ; Salinity ; Salt Tolerance ; Sodium Chloride/metabolism ; Archaea/metabolism/drug effects ; },
abstract = {Haloarchaea, known for their resilience to environmental fluctuations, require a minimum salt concentration of 10% (w/v) for growth and can survive up to 35% (w/v) salinity. In biotechnology, these halophiles have diverse industrial applications. This study investigates the tolerance responses of nine haloarchaea: Haloferax mediterranei, Haloferax volcanii, Haloferax gibbonsii, Halorubrum californiense, Halorubrum litoreum, Natrinema pellirubrum, Natrinema altunense, Haloterrigena thermotolerans and Haloarcula sinaiiensis, under various stressful conditions. All these archaea demonstrated the ability to thrive in the presence of toxic metals such as chromium, nickel, cobalt and arsenic, and their tolerance to significantly elevated lithium concentrations in the medium was remarkable. Among the studied haloarchaea, Hfx. mediterranei exhibited superior resilience, particularly against lithium, with an impressive minimum inhibitory concentration (MIC) of up to 4 M LiCl, even replacing NaCl entirely. Haloferax species showed specificity for conditions with maximal growth rates, while Htg. thermotolerans and Nnm. altunense displayed high resilience without losing growth throughout the ranges, although these were generally low. ICP-MS results highlighted the impressive intracellular lithium accumulation in Nnm. pellirubrum, emphasizing its potential significance in bioremediation. This research highlights a new characteristic of haloarchaea, their tolerance to high lithium concentrations and the potential for new applications in extreme industrial processes and bioremediation.},
}

*Stress, Physiological
Salinity
Salt Tolerance
Sodium Chloride/metabolism
Archaea/metabolism/drug effects

@article {pmid39567663,
year = {2024},
author = {Nobu, MK},
title = {Engineering history with Asgard archaea of the kingdom Promethearchaeati.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39567663},
issn = {2058-5276},
}

@article {pmid39562414,
year = {2024},
author = {Kemp, JA and Schultz, J and Modolon, F and Ribeiro-Alves, M and Rosado, AS and Mafra, D},
title = {Is there a correlation between TMAO plasma levels and archaea in the gut of patients undergoing hemodialysis?.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {39562414},
issn = {1573-2584},
abstract = {PURPOSE: Patients with chronic kidney disease (CKD) present high plasma levels of trimethylamine N-oxide (TMAO), a uremic toxin produced by gut microbiota associated with atherogenesis. Experimental studies have shown that certain methanogenic archaea members use trimethylamine (TMA), the TMAO precursor in the human gut, to produce methane, suggesting a potential strategy to reduce TMAO levels in patients with CKD. Hence, this study aimed to evaluate the association of Archaea in the gut microbiota and TMAO plasma levels in patients with CKD undergoing hemodialysis.

METHODS: Twenty-five patients were enrolled in the study (15 women, 53 (18) years, BMI, 25.8 (6.75) kg/m[2]). TMAO plasma levels were evaluated using the HPLC-EM/EM method. Fecal DNA was extracted using a commercial kit. Subsequently, we sequenced the V4 region of the 16S rRNA gene to characterize the microbial composition. NCT04600258 was retrospectively registered in September 2022.

RESULTS: According to the reference values in the European Uremic Toxins Work Group (EUTox) database, the patients exhibited high TMAO plasma levels, as expected. The most abundant Archaea members were assigned to the Euryarchaeota phylum, the Methanobacteriaceae family, and the genus Methanobrevibacter. A significant negative correlation between TMAO and Methanobrevibacter was observed.

CONCLUSIONS: To our knowledge, this study represents the first investigation into the correlation between TMAO levels and the prevalence of Archaea in patients with CKD. Our findings support the archaebiotic hypothesis, suggesting that specific members of the archaea community could play a crucial role in reducing TMA production in the human gut, potentially decreasing TMAO synthesis in CKD patients.},
}

@article {pmid39560730,
year = {2024},
author = {Liang, Y and Yan, Y and Shi, L and Wang, M and Yuan, X and Wang, S and Ye, L and Yan, Z},
title = {Molecular Basis of Thioredoxin-Dependent Arsenic Transformation in Methanogenic Archaea.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c06611},
pmid = {39560730},
issn = {1520-5851},
abstract = {Methanogenic archaea are known to play a crucial role in the biogeochemical cycling of arsenic (As); however, the molecular basis of As transformation mediated by methanogenic archaea remains poorly understood. Herein, the characterization of the redox transformation and methylation of As by Methanosarcina acetivorans, a model methanogenic archaeon, is reported. M. acetivorans was demonstrated to mediate As(V) reduction via a cytoplasmic As reductase (ArsC) in the exponential phase of methanogenic growth and to methylate As(III) via a cytoplasmic As(III) methyltransferase (ArsM) in the stationary phase. Characterization of the ArsC-catalyzed As(V) reduction and the ArsM-catalyzed As(III) methylation showed that a thioredoxin (Trx) encoded by MA4683 was preferentially utilized as a physiological electron donor for ArsC and ArsM, providing a redox link between methanogenesis and As transformation. The structures of ArsC and ArsM complexed with Trx were modeled using AlphaFold-Multimer. Site-directed mutagenesis of key cysteine residues at the interaction sites of the complexes indicated that the archaeal ArsC and ArsM employ evolutionarily distinct disulfide bonds for interacting with Trx compared to those used by bacterial ArsC or eukaryotic ArsM. The findings of this study present a major advance in our current understanding of the physiological roles and underlying mechanism of As transformation in methanogenic archaea.},
}

@article {pmid39545734,
year = {2024},
author = {Xu, T and Ni, Y and Li, H and Wu, S and Yan, S and Chen, L and Yu, Y and Wang, Y},
title = {Discovery and characterization of complete genomes of 38 head-tailed proviruses in four predominant phyla of archaea.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0049224},
doi = {10.1128/spectrum.00492-24},
pmid = {39545734},
issn = {2165-0497},
abstract = {Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert a considerable influence on the structure and composition of archaeal communities and their associated ecological environments. The present study revealed the complete genomes of 38 archaeal head-tailed proviruses through comprehensive data mining. The hosts of these proviruses were identified as belonging to the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. In addition to the 14 proviruses of halophilic archaea related to the Graaviviridae family, the remaining proviruses exhibited limited genetic similarities to known (pro)viruses, suggesting the existence of 14 potential novel families. Of the 38 archaeal proviruses, 30 have the potential to lyse host cells. Eleven proviruses contain genes linked to antiviral defense mechanisms, including those involved in restriction modification (RM), clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) nucleases, defense island system associated with restriction-modification (DISARM), and DNA degradation (Dnd). Moreover, auxiliary metabolic genes were identified in the proviruses of Bathyarchaeia and Halobacteriota archaea, including those involved in carbohydrate and amino acid metabolism. Our findings indicate the diversity of archaeal viruses, their interactions with archaeal hosts, and their roles in the adaptation of the host.IMPORTANCEThe field of archaeal virology has seen a rapid expansion through the use of metagenomics, yet the diversity of these viruses remains largely uncharted. In this study, the complete genomes of 38 novel archaeal proviruses were identified for the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. Two families and six genera of Archaea were the first to be identified as hosts for viruses. The proviruses were found to contain diverse genes that were involved in distinct adaptation strategies of viruses to hosts. Our findings contribute to the expansion of the lineages of archaeal viruses and highlight their intricate interactions and essential roles in enabling host survival and adaptation to diverse environmental conditions.},
}

@article {pmid39544964,
year = {2024},
author = {Abiola, C and Gwak, JH and Lee, UJ and Awala, SI and Jung, MY and Park, W and Rhee, SK},
title = {Growth of soil ammonia-oxidizing archaea on air-exposed solid surface.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae129},
pmid = {39544964},
issn = {2730-6151},
abstract = {Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOMs), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), Nitrososphaera viennensis EN76 and "Nitrosotenuis chungbukensis" MY2, and a soil ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of N. viennensis EN76 and "N. chungbukensis" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of N. europaea ATCC 19718 was comparable on floating filters and liquid media. N. viennensis EN76 and N. europaea ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of N. viennensis EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, ammonia oxidation (including ammonia monooxygenase subunit C (amoC3) and multicopper oxidases), and defense against H2O2-induced oxidative stress. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the "Ca. Nitrosocosmicus" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.},
}

@article {pmid39541851,
year = {2024},
author = {Wang, F and Huang, W and Chen, J and Luo, Y and Cao, J and Fang, F and Liu, X and Wu, Y and Luo, J},
title = {Non-antibiotic disinfectant synchronously interferes methane production and antibiotic resistance genes propagation during sludge anaerobic digestion: Activation of microbial adaptation and reconfiguration of bacteria-archaea synergies.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122773},
doi = {10.1016/j.watres.2024.122773},
pmid = {39541851},
issn = {1879-2448},
abstract = {Waste activated sludge (WAS) presents both resource recovery potential and pollution risks, making its efficient treatment challenging. Anaerobic digestion is broadly recognized as a green and sustainable approach to WAS treatment, whose efficiency is easily impacted by the exogeneous pollutants in WAS. However, the impact of polyhexamethylene guanidine (PHMG), as a widely-used non-antibiotic disinfectant, on WAS digestion under semi-continuous flow conditions remains unclear. In this study, CH4 production decreased from 16.1 mL/g volatile suspended solids (VSS) in the control to 13.2 mL/g VSS and 0.3 mL/g VSS under low and high PHMG exposure, respectively, while PHMG increased the number of antibiotic resistance gene (ARG) copies per bacterium by 4.6-12.7 %. Molecular docking analysis revealed that PHMG could spontaneously bind to and disintegrate WAS (binding energy:2.35 and -9.62 kcal/mol), increasing the likelihood of microbial exposure to PHMG. This led to an increase in bacterial abundance and a reduction in archaeal populations, resulting in bacterial dominance in ecological niches. The network topology index in PHMG-treated reactors was consistently lower than in the control, with a higher proportion of negatively correlated links, indicating a more antagonistic relationship between bacteria and archaea. Consequently, PHMG significantly interfered with key genes involved in CH4 biosynthesis (e.g., mch and mtd). Interestingly, methanogenic activity and archaeal chemotaxis (e.g., rfk and cheA) partially recovered under low PHMG exposure due to archaeal adaptation through quorum sensing and two-component systems. However, this adaptation process also contributed to the propagation of ARGs through horizontal gene transfer, facilitated by the enhancement of mobile genetic elements and ARGs hosts. These findings confirm the ecological risks of PHMG and highlight the need for effective WAS disposal strategies.},
}

@article {pmid39514410,
year = {2024},
author = {Dodsworth, JA and Prakash, O},
title = {International Committee on Systematics of Prokaryotes: subcommittee on the taxonomy of methanogenic archaea. Minutes of the closed, online meeting held 06 September 2023.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006569},
pmid = {39514410},
issn = {1466-5034},
}

@article {pmid39511174,
year = {2024},
author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F},
title = {Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9628},
pmid = {39511174},
issn = {2041-1723},
support = {NNF22OC0071609//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; ERC-RA-0020//Helmholtz Association/ ; 101059607//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 12471341//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Oxidation-Reduction ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Butanes/metabolism ; *Carbon Dioxide/metabolism ; Oxidoreductases/metabolism/genetics ; Kinetics ; Alkanes/metabolism ; Thermodynamics ; },
abstract = {Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery of archaea oxidizing volatile alkanes via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis of archaea-catalysed alkane formation in nature (alkanogenesis). A combination of metabolic modelling, anaerobic physiology assays, and isotope labeling of Candidatus Syntrophoarchaeum archaea catalyzing the anaerobic oxidation of butane (AOB) show a back flux of CO2 to butane, demonstrating reversibility of the entire AOB pathway. Back fluxes correlate with thermodynamics and kinetics of the archaeal catabolic system. AOB reversibility supports a biological formation of butane, and generally of higher volatile alkanes, helping to explain the presence of isotopically light alkanes and deeply branching ACR genes in sedimentary basins isolated from gas reservoirs.},
}

*Oxidation-Reduction
Anaerobiosis
*Archaea/metabolism/genetics
*Butanes/metabolism
*Carbon Dioxide/metabolism
Oxidoreductases/metabolism/genetics
Kinetics
Alkanes/metabolism
Thermodynamics

@article {pmid39530672,
year = {2024},
author = {Lee, U-J and Gwak, J-H and Choi, S and Jung, M-Y and Lee, TK and Ryu, H and Imisi Awala, S and Wanek, W and Wagner, M and Quan, Z-X and Rhee, S-K},
title = {"Ca. Nitrosocosmicus" members are the dominant archaea associated with plant rhizospheres.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0082124},
doi = {10.1128/msphere.00821-24},
pmid = {39530672},
issn = {2379-5042},
abstract = {UNLABELLED: Archaea catalyzing the first step of nitrification in the rhizosphere possibly have an influence on plant growth and development. In this study, we found a distinct archaeal community, dominated by ammonia-oxidizing archaea (AOA), associated with the root system of pepper (Capsicum anuum L.) and ginseng plants (Panax ginseng C.A. Mey.) compared to bulk soil not penetrated by roots. While the abundance of total AOA decreased in the rhizosphere soils, AOA related to "Candidatus Nitrosocosmicus," which harbor gene encoding manganese catalase (MnKat) in contrast to most other AOA, dominated the AOA community in the rhizosphere soils. For both plant species, the ratio of copy numbers of the AOA MnKat gene to the amoA gene (encoding the ammonia monooxygenase subunit A) was significantly higher in the rhizospheres than in bulk soils. In contrast to MnKat-negative strains from other AOA clades, the catalase activity of a representative isolate of "Ca. Nitrosocosmicus" was demonstrated. Members of this clade were enriched in H2O2-amended bulk soils, and constitutive expression of their MnKat gene was observed in both bulk and rhizosphere soils. Due to their abundance, "Ca. Nitrosocosmicus" members can be considered important players mediating the nitrification process in rhizospheres. The dominance of this MnKat-containing AOA in rhizospheres of agriculturally important plants hints at a previously overlooked AOA-plant interaction.

IMPORTANCE: Ammonia-oxidizing archaea (AOA) are widespread in terrestrial environments and outnumber other ammonia oxidizers in the rhizosphere, possibly exerting an influence on plant growth and development. However, little is known about the selection forces that shape their composition, functions, survival, and proliferation strategies in the rhizosphere. Here, we observed a distinct AOA community on root systems of two different plant species compared to bulk soil. Our results show that the "Ca. Nitrosocosmicus" clade, which possesses functional MnKat genes unlike most other AOA, dominated the rhizosphere soils. Moreover, members of this clade were enriched in H2O2-amended bulk soil, which mimics the ROS stress in root systems. While research on AOA-plant interactions in the rhizosphere is still in its infancy, these findings suggest that "Ca. Nitrosocosmicus" may be an important clade of AOA with potential AOA-plant interaction.},
}

@article {pmid39529672,
year = {2024},
author = {Hernández-Magaña, E and Kraft, B},
title = {Corrigendum: Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1506979},
doi = {10.3389/fmicb.2024.1506979},
pmid = {39529672},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1410251.].},
}

@article {pmid39499858,
year = {2024},
author = {Takamiya, H and Kouduka, M and Kato, S and Suga, H and Oura, M and Yokoyama, T and Suzuki, M and Mori, M and Kanai, A and Suzuki, Y},
title = {Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae207},
pmid = {39499858},
issn = {1751-7370},
mesh = {*Hydrothermal Vents/microbiology ; *Archaea/genetics/metabolism/classification/isolation & purification ; *Genome, Archaeal ; Phylogeny ; Metagenomics ; Proteomics ; Ecosystem ; },
abstract = {Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we investigated a deep-sea hydrothermal vent chimney without fluid venting where our previous study revealed the high proportion of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea. Using spectroscopic methods with submicron soft X-ray and infrared beams, the microbial habitat was specified to be silica-filled pores in the inner chimney wall comprising chalcopyrite. Metagenomic analysis of the inner wall revealed the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids in the Pacearchaeota genomes. Genome-resolved metaproteomic analysis clarified the co-occurrence of a novel thermophilic lineage actively fixing carbon and nitrogen and thermophilic archaea in the inner chimney wall. We infer that the shift in metabolically active microbial populations from the thermophiles to the mesophilic DPANN archaea occurs after the termination of fluid venting. The infilling of mineral pores by hydrothermal silica deposition might be a preferred environmental factor for the colonization of free-living Pacearchaeota with ultrasmall cells depending on metabolites synthesized by the co-occurring thermophiles during fluid venting.},
}

*Hydrothermal Vents/microbiology
*Archaea/genetics/metabolism/classification/isolation & purification
*Genome, Archaeal
Phylogeny
Metagenomics
Proteomics
Ecosystem

@article {pmid39499655,
year = {2024},
author = {Medvedeva, S and Borrel, G and Gribaldo, S},
title = {Sheaths are diverse and abundant cell surface layers in archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae225},
pmid = {39499655},
issn = {1751-7370},
abstract = {Prokaryotic cells employ multiple protective layers crucial for defense, structural integrity, and cellular interactions in the environment. Archaea often feature an S-layer, with some species possessing additional and remarkably resistant sheaths. The archaeal sheath has been studied in Methanothrix and Methanospirillum, revealing a complex structure consisting of amyloid proteins organized into rings. Here, we conducted a comprehensive survey of sheath-forming proteins (SH proteins) across archaeal genomes. Structural modeling reveals a rich diversity of SH proteins, indicating the presence of a sheath in members of the TACK superphylum (Thermoprotei), as well as in the methanotrophic ANME-1. SH proteins are present in up to 40 copies per genome and display diverse domain arrangements suggesting multifunctional roles within the sheath, and potential involvement in cell-cell interaction with syntrophic partners. We uncover a complex evolutionary dynamic, indicating active exchange of SH proteins in archaeal communities. We find that viruses infecting sheathed archaea encode a diversity of SH-like proteins and we use them as markers to identify 580 vOTUs potentially associated with sheathed archaea. Structural modeling suggests that viral SH proteins can form complexes with the host SH proteins. We propose a previously unreported egress strategy where the expression of viral SH-like proteins may disrupt the integrity of the host sheath and facilitate viral exit during lysis. Together, our results significantly expand knowledge of the diversity and evolution of the archaeal sheath, which has been largely understudied but might have an important role in shaping microbial communities.},
}

@article {pmid39495356,
year = {2024},
author = {Ma, X and Hu, Y and Hou, J and Zhou, YG and Cui, HL},
title = {Genome-Based Classification of 'Haloarcula aidinensis' and Description of Three Novel Halophilic Archaea Isolated from an Inland Saline Lake, Coastal Saline Soil, and a Marine Solar Saltern.},
journal = {Current microbiology},
volume = {81},
number = {12},
pages = {442},
pmid = {39495356},
issn = {1432-0991},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Haloarcula/genetics/classification ; *Genome, Archaeal ; China ; *Lakes/microbiology ; *Soil Microbiology ; DNA, Archaeal/genetics/chemistry ; RNA, Ribosomal, 16S/genetics ; Phospholipids/analysis ; Sequence Analysis, DNA ; },
abstract = {'Haloarcula aidinensis' was described by a pioneer Chinese scientist focused on halophilic archaea thirty years ago, and the type strain of 'Haloarcula aidinensis' was recently classified based on phylogenetic, phylogenomic, and comparative genomic analyses. Other three novel halophilic archaeal strains, CK38[T], DT43[T], and SYNS111[T], isolated from diverse saline environments in China, were simultaneously subjected to polyphasic classification. 'Haloarcula aidinensis' A5 was found to be related to Haloarcula amylolytica, while strains CK38[T], DT43[T], and SYNS111[T] represented three novel species of Haloarcula based on phylogenetic, phylogenomic, and comparative genomic analyses. These strains can be distinguished from other species within the genus Haloarcula based on multiple phenotypic characteristics. The major phospholipids, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and phosphatidylglycerol sulfate can be detected in these strains, while the glycolipid profiles of these strains are diverse. Strains A5 and DT43[T] contained glucosyl mannosyl glucosyl diether and a diglycosyl diether, while other strains CK38[T] and SYNS111[T] had sulfated mannosyl glucosyl diether and mannosyl glucosyl diether. Thus, strain A5 should be a reference strain of Har. amylolytica and three novel species of Haloarcula, Haloarcula sediminis sp. nov., Haloarcula brevis sp. nov., and Haloarcula regularis sp. nov. are proposed to accommodate strains CK38[T] (= CGMCC 1.62732[T] = JCM 36675[T]), DT43[T] (= CGMCC 1.18924[T] = JCM 36146[T]), and SYNS111[T] (= CGMCC 1.62601[T] = JCM 36149[T]).},
}

*Phylogeny
*Haloarcula/genetics/classification
*Genome, Archaeal
China
*Lakes/microbiology
*Soil Microbiology
DNA, Archaeal/genetics/chemistry
RNA, Ribosomal, 16S/genetics
Phospholipids/analysis
Sequence Analysis, DNA

@article {pmid39490771,
year = {2024},
author = {Li, T and Coker, OO and Sun, Y and Li, S and Liu, C and Lin, Y and Wong, SH and Miao, Y and Sung, JJ and Yu, J},
title = {Multi-cohort analysis reveals altered archaea in colorectal cancer fecal samples across populations.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2024.10.023},
pmid = {39490771},
issn = {1528-0012},
abstract = {BACKGROUND AND AIM: Archaea are important components of the host microbiome, but their roles in colorectal cancer (CRC) remain largely unclear. We aimed to elucidate the contribution of gut archaea to CRC across multiple populations.

METHODS: This study incorporated fecal metagenomic data from 10 independent cohorts from 7 countries and an additional in-house cohort, totaling 2101 metagenomes (748 CRC, 471 adenoma, and 882 healthy controls (HC)). Taxonomic profiling was performed using Kraken2 against the Genome Taxonomy Database. Alterations of archaeal communities and their interactions with bacteria and methanogenic functions were analyzed. Random Forest model was used to identify multicohort diagnostic microbial biomarkers in CRC.

RESULTS: The overall archaeal alpha diversity shifted from HC, adenoma patients to CRC patients with Methanobacteriota phylum enriched while order Methanomassiliicoccales depleted. At the species level, Methanobrevibacter_A smithii and Methanobrevibacter_A sp002496065 were enriched, while 8 species, including Methanosphaera stadtmanae and Methanomassiliicoccus_A intestinalis, were depleted in CRC patients across multiple cohorts. Among them, M. stadmanae, Methanobrevibacter_A sp900314695 and Methanocorpusculum sp001940805 exhibited a progressive decrease in the HC-adenoma-CRC sequence. CRC-depleted methanogenic archaea exhibited enhanced co-occurring interactions with butyrate-producing bacteria. Consistently, methanogenesis-related genes and pathways were enriched in CRC patients. A model incorporating archaeal and bacterial biomarkers outperformed single-kingdom models in discriminating CRC patients from healthy individuals with AUC ranging from 0.744 to 0.931 in leave-one-cohort-out analysis.

CONCLUSIONS: This multicohort analysis uncovered significant alterations in gut archaea and their interactions with bacteria in healthy individuals, adenoma patients and CRC patients. Archaeal biomarkers, combined with bacterial features, have potential as non-invasive diagnostic biomarkers for CRC.},
}

@article {pmid39486247,
year = {2024},
author = {Ma, JY and Jiang, YQ and Liu, XY and Sun, XD and Jia, YN and Wang, Y and Tan, MM and Duan, JL and Yuan, XZ},
title = {Amplified selenite toxicity in methanogenic archaea mediated by cysteine.},
journal = {Ecotoxicology and environmental safety},
volume = {287},
number = {},
pages = {117263},
doi = {10.1016/j.ecoenv.2024.117263},
pmid = {39486247},
issn = {1090-2414},
abstract = {The challenge of understanding the interaction between trace elements and microbial life is critical for assessing environmental and ecological impacts. Nevertheless, cysteine (Cys), a low molecular weight thiol substance prevalent in the ecosystem, is able to influence the fate of certain trace elements, which increases the complexity of the interaction between trace elements and microorganisms. Therefore, we chose Cys, selenite and the model methanogenic archaeon Methanosarcina acetivorans C2A as research targets, and comprehensively explored the intricate role of Cys in modulating the biological effects of selenite on M. acetivorans C2A in terms of population growth, methane production and oxidative stress. Our results demonstrate that Cys significantly exacerbates the inhibitory effects of selenite on growth and methane production in M. acetivorans C2A. This increased toxicity is linked to heightened membrane permeability and oxidative stress, with a marked upregulation in reactive oxygen species and changes in NADPH levels. Transcriptomic analysis reveals alterations in genes associated with transmembrane transport and methanogenesis. Intriguingly, we also observed a potential interaction between selenite and phosphate transmembrane transporters, suggesting a novel pathway for selenite entry into cells. These findings highlight the complex interplay between trace elements and microbial processes, with significant implications for understanding environmental risks and developing remediation strategies.},
}

@article {pmid39466404,
year = {2024},
author = {Ortjohann, M and Schönheit, P},
title = {Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {3},
pages = {48},
pmid = {39466404},
issn = {1433-4909},
mesh = {*Haloarcula/metabolism/genetics ; *Sorbitol/metabolism ; *Mannitol/metabolism ; Archaeal Proteins/metabolism/genetics ; Fructokinases/metabolism/genetics ; Fructose/metabolism ; ATP-Binding Cassette Transporters/metabolism/genetics ; },
abstract = {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 ketohexokinase, providing the first evidence for a physiological function of ketohexokinase in prokaryotes. Finally, fructose-1-phosphate is phosphorylated via fructose-1-phosphate kinase to fructose-1,6-bisphosphate, which is cleaved to triosephosphates by a Class I fructose-1,6-bisphosphate aldolase. Two distinct transcriptional regulators, acting as activators, have been identified: an IclR-like regulator involved in activating genes for sugar alcohol uptake and oxidation to fructose, and a GfcR-like regulator that likely activates genes involved in the degradation of fructose to pyruvate. This is the first comprehensive analysis of a sugar alcohol degradation pathway in Archaea.},
}

*Haloarcula/metabolism/genetics
*Sorbitol/metabolism
*Mannitol/metabolism
Archaeal Proteins/metabolism/genetics
Fructokinases/metabolism/genetics
Fructose/metabolism
ATP-Binding Cassette Transporters/metabolism/genetics

@article {pmid39455151,
year = {2024},
author = {Pan, YC and Zhao, JW and Niu, HJ and Huang, YL and Wang, Y and Zhang, XX},
title = {[Effects of Vegetable Planting Ages on Community Structure of Ammonia-oxidizing Archaea and Ammonia-oxidizing Bacteria in Greenhouse Vegetable Fields].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {10},
pages = {6077-6085},
doi = {10.13227/j.hjkx.202310135},
pmid = {39455151},
issn = {0250-3301},
mesh = {*Archaea/metabolism/growth & development/classification ; *Ammonia/metabolism ; *Soil Microbiology ; *Bacteria/classification/growth & development/metabolism ; *Oxidation-Reduction ; *Vegetables/growth & development ; Soil/chemistry ; China ; Nitrous Oxide/metabolism/analysis ; Time Factors ; Agriculture/methods ; Nitrogen/metabolism ; },
abstract = {The ammonia oxidation process driven by microorganisms is a dominant source for nitrous oxide （N2O） emissions. Here, we examined the influence of greenhouse vegetable planting ages on soil ammonia-oxidizing archaea （AOA） and ammonia-oxidizing bacteria （AOB）, which is of great significance for assessing the soil quality status and greenhouse gas transformations. A field study was conducted at different times （1, 5, 10, and 20 a） in greenhouse vegetable soils of Gaoyi, Hebei Province. Chemical analysis and Illumina NovaSeq high-throughput sequencing were used to analyze the soil physicochemical properties and community structures and diversity of AOA and AOB. The variation in AOA and AOB communities and the driving factors in greenhouse soils at different ages were also investigated. The results showed that the contents of total nitrogen, organic matter, alkali-hydrolyzable nitrogen, available phosphorus, and available potassium first increased and then decreased with the prolongation of growth. The contents of nitrate nitrogen, ammonium nitrogen, and electrical conductivity first decreased and then increased with the prolongation of growth. The pH value of soils decreased with the prolongation of growth. The abundance and diversity index of AOA and AOB first decreased and then increased with the prolongation of growth. Nitrososphaeria, unclassified Thaumarchaeota, and Candidatus Nitrosocaldus were the dominant species of AOA, while Betaproteobacteria and Nitrosospira were the dominant species of AOB. The composition of the soil AOA community varied greatly compared to that of AOB with the prolongation of growth. Correlation analysis showed that the changes in soil nutrient factors had a significant correlation with AOA and AOB communities. Redundancy analysis indicated that ammonium nitrogen, alkali-hydrolyzable nitrogen, and nitrate nitrogen were key factors of AOA communities, while electrical conductivity, available potassium, and nitrate nitrogen were key factors for AOB. In summary, long-term planting of greenhouse vegetables significantly affected the abundance and composition of soil AOA and AOB communities. Our results provide a theoretical basis for further studies on the greenhouse gas transformation and microbial mechanisms of the nitrogen cycle in greenhouse soils.},
}

*Archaea/metabolism/growth & development/classification
*Ammonia/metabolism
*Soil Microbiology
*Bacteria/classification/growth & development/metabolism
*Oxidation-Reduction
*Vegetables/growth & development
Soil/chemistry
China
Nitrous Oxide/metabolism/analysis
Time Factors
Agriculture/methods
Nitrogen/metabolism

@article {pmid39437693,
year = {2024},
author = {Zhang, L and Yang, J and Ge, AH and Xie, W and Yao, R and Wang, X},
title = {Salinity drives niche differentiation of soil bacteria and archaea in Hetao Plain, China.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122977},
doi = {10.1016/j.jenvman.2024.122977},
pmid = {39437693},
issn = {1095-8630},
abstract = {Soil salinization is a critical environmental issue that limits plant productivity and disrupts ecosystem functions. As important indicators of soil environment, soil microbes play essential roles in driving nutrient cycling and sustaining ecosystem services. Therefore, understanding how microbial communities and their functional potentials respond to varying levels of soil salinization across different land use types is crucial for the restoration and management of salt-affected ecosystems. In this study, we randomly selected 63 sites across the Hetao Plain, covering an area of ∼2500 km[2]. Our results showed that both salinity- and fertility-related soil parameters were significantly correlated with bacterial and archaeal diversities, with soil salinity emerging as the stronger predictor of prokaryotic diversity. Intriguingly, bacterial and archaeal communities were tightly interlinked but displayed opposite trends in response to environmental factors, indicating a clear microbial niche differentiation driven by soil salinity. Moreover, the generalist functions of bacteria and archaea (e.g., chemoheterotrophy) exhibited contrasting responses to environmental parameters, while their specialist functions (e.g., nitrification) responded consistently. These findings highlight the pivotal role of soil salinity in shaping the niche differentiation of bacterial and archaeal communities in saline soils, providing insights to guide salinity-centered restoration strategies for effective marginal land management.},
}

@article {pmid39436425,
year = {2024},
author = {Dong, XY and Mao, YL and Zhang, QK and Zhu, LR and Hou, J and Cui, HL},
title = {Genome‑based classification of the family Natrialbaceae and description of four novel halophilic archaea from three saline lakes and a saline-alkaline land.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {3},
pages = {47},
pmid = {39436425},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Genome, Archaeal ; *Lakes/microbiology ; Halobacteriales/genetics/classification ; Salt Tolerance ; Salinity ; },
abstract = {The current representatives of the family Natrialbaceae within the class Halobacteria were subjected to phylogenetic, phylogenomic, and comparative genomic analyses. The current species of Halobiforma and Halomontanus were found to be related to those of Natronobacterium and Natronoglomus, respectively. According to the cutoff value of average amino acid identity (AAI) (≤ 76%) proposed to differentiate genera within the family Natrialbaceae, Halobiforma, and Natronoglomus should be merged with Natronobacterium and Halomontanus, respectively. Beyond these, four novel halophilic archaeal strains, CCL63[T], AD-5[T], CG52[T], and KLK7[T], isolated from three saline lakes and a saline-alkaline land in China, were simultaneously subjected to polyphasic classification. The phenotypic, phylogenetic, phylogenomic, and comparative genomic analyses indicated that strain CCL63[T] (= CGMCC 1.18663[T] = JCM 35096[T]) represents a novel genus of the family Natrialbaceae, strains AD-5[T] (= CGMCC 1.13783[T] = JCM 33734[T]) and CG52[T] (= CGMCC 1.17139[T] = JCM 34160[T]) represent two novel species of the genus Natronococcus, and strain KLK7[T] (= MCCC 4K00128[T] = KCTC 4307[T]) represents a novel species of Haloterrigena. Halovalidus salilacus gen. nov., sp. nov., Natronococcus wangiae sp. nov., Natronococcus zhouii sp. nov., and Haloterrigena salinisoli sp. nov. are further proposed based on these type strains accordingly.},
}

*Phylogeny
*Genome, Archaeal
*Lakes/microbiology
Halobacteriales/genetics/classification
Salt Tolerance
Salinity

@article {pmid39433727,
year = {2024},
author = {Lemaire, ON and Wegener, G and Wagner, T},
title = {Ethane-oxidising archaea couple CO2 generation to F420 reduction.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9065},
pmid = {39433727},
issn = {2041-1723},
support = {WA 4053/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WE 5492/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WA 4053/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Oxidation-Reduction ; *Carbon Dioxide/metabolism ; *Ethane/metabolism/chemistry ; Archaea/metabolism/genetics ; Aldehyde Oxidoreductases/metabolism/genetics/chemistry ; Multienzyme Complexes/metabolism/genetics/chemistry ; Crystallography, X-Ray ; Archaeal Proteins/metabolism/genetics/chemistry ; Anaerobiosis ; Ferredoxins/metabolism ; Riboflavin/analogs & derivatives ; },
abstract = {The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO2-forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO2-generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F420 reductase. Accordingly, both systems exhibit robust coupled F420-reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy.},
}

*Oxidation-Reduction
*Carbon Dioxide/metabolism
*Ethane/metabolism/chemistry
Archaea/metabolism/genetics
Aldehyde Oxidoreductases/metabolism/genetics/chemistry
Multienzyme Complexes/metabolism/genetics/chemistry
Crystallography, X-Ray
Archaeal Proteins/metabolism/genetics/chemistry
Anaerobiosis
Ferredoxins/metabolism
Riboflavin/analogs & derivatives

@article {pmid39413712,
year = {2024},
author = {Wang, M and Peñuelas, J and Sardans, J and Zeng, Q and Song, Z and Zhou, J and Xu, X and Zhou, X and Fang, Y and Vancov, T and Wang, W},
title = {Conversion of coastal marsh to aquaculture ponds decreased the potential of methane production by altering soil chemical properties and methanogenic archaea community structure.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122608},
doi = {10.1016/j.watres.2024.122608},
pmid = {39413712},
issn = {1879-2448},
abstract = {Coastal wetlands are among the most productive and dynamic ecosystems globally, contributing significantly to atmospheric methane (CH4) emissions. The widespread conversion of these wetlands into aquaculture ponds degrades these ecosystems, yet its effects on CH4 production and associated microbial mechanisms are not well understood. This study aimed to assess the impact of land conversion on CH4 production potential, total and active soil organic C (SOC) content, and microbial communities. We conducted a comparative study on three brackish marshes and adjacent aquaculture ponds in southeastern China. Compared to costal marshes, aquaculture ponds exhibited significantly (P < 0.05) lower CH4 production potential (0.05 vs. 0.02 μg kg[-1] h[-1]), SOC (17.64 vs. 6.97 g kg[-1]), total nitrogen (TN) content (1.62 vs. 1.24 g kg[-1]) and carbon/nitrogen (C/N) ratio (10.85 vs. 5.66). CH4 production potential in aquaculture ponds was influenced by both microbial and abiotic factors. Specifically, the relative abundance of Methanosarcina slightly decreased in aquaculture ponds, while the potential for CH4 production declined with lower SOC contents and C/N ratio. Overall, our findings demonstrate that converting natural coastal marshes into aquaculture ponds reduces CH4 production by altering key soil properties and the structure and diversity of methanogenic archaea communities. These results provide empirical evidence to enhance global carbon models, improving predictions of carbon feedback from wetland land conversion in the context of climate change.},
}

@article {pmid39406503,
year = {2024},
author = {Valentin-Alvarado, LE and Shi, LD and Appler, KE and Crits-Christoph, A and De Anda, V and Adler, BA and Cui, ML and Ly, L and Leão, P and Roberts, RJ and Sachdeva, R and Baker, BJ and Savage, DF and Banfield, JF},
title = {Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279480.124},
pmid = {39406503},
issn = {1549-5469},
abstract = {Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth-resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.},
}

@article {pmid39404452,
year = {2024},
author = {Villa, EA and Escalante-Semerena, JC},
title = {Corrinoid salvaging and cobamide remodeling in bacteria and archaea.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0028624},
doi = {10.1128/jb.00286-24},
pmid = {39404452},
issn = {1098-5530},
abstract = {Cobamides (Cbas) are cobalt-containing cyclic tetrapyrroles used by cells from all domains of life as co-catalyst of diverse reactions. There are several structural features that distinguish Cbas from one another. The most relevant of those features discussed in this review is the lower ligand, which is the nucleobase of a ribotide located in the lower face of the cyclic tetrapyrrole ring. The above-mentioned ribotide is known as the nucleotide loop, which is attached to the ring by a short linker. In Cbas, the nucleobase of the ribotide can be benzimidazole or derivatives of it, purine or derivatives of it, or phenolic compounds. Given the importance of Cbas in prokaryotic metabolism, it is not surprising that prokaryotes have evolved enzymes that cleave part or the entire nucleotide loop. This function is advantageous when Cbas contain nucleobases that somehow interfere with the function of Cba-dependent enzymes in the organism. After cleavage, Cbas are rebuilt via the nucleotide loop assembly (NLA) pathway, which includes enzymes that activate the nucleobase and the ring intermediate, followed by condensation of activated intermediates and a final dephosphorylation reaction. This exchange of nucleobases is known as Cba remodeling. The NLA pathway is used to salvage Cba precursors from the environment.},
}

@article {pmid39402493,
year = {2024},
author = {Bobbo, T and Biscarini, F and Yaddehige, SK and Alberghini, L and Rigoni, D and Bianchi, N and Taccioli, C},
title = {Machine learning classification of archaea and bacteria identifies novel predictive genomic features.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {955},
pmid = {39402493},
issn = {1471-2164},
mesh = {*Archaea/genetics/classification ; *Machine Learning ; *Bacteria/genetics/classification ; *Genomics/methods ; *Genome, Archaeal ; Genome, Bacterial ; RNA, Transfer/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Archaea and Bacteria are distinct domains of life that are adapted to a variety of ecological niches. Several genome-based methods have been developed for their accurate classification, yet many aspects of the specific genomic features that determine these differences are not fully understood. In this study, we used publicly available whole-genome sequences from bacteria (N = 2546) and archaea (N = 109). From these, a set of genomic features (nucleotide frequencies and proportions, coding sequences (CDS), non-coding, ribosomal and transfer RNA genes (ncRNA, rRNA, tRNA), Chargaff's, topological entropy and Shannon's entropy scores) was extracted and used as input data to develop machine learning models for the classification of archaea and bacteria.

RESULTS: The classification accuracy ranged from 0.993 (Random Forest) to 0.998 (Neural Networks). Over the four models, only 11 examples were misclassified, especially those belonging to the minority class (Archaea). From variable importance, tRNA topological and Shannon's entropy, nucleotide frequencies in tRNA, rRNA and ncRNA, CDS, tRNA and rRNA Chargaff's scores have emerged as the top discriminating factors. In particular, tRNA entropy (both topological and Shannon's) was the most important genomic feature for classification, pointing at the complex interactions between the genetic code, tRNAs and the translational machinery.

CONCLUSIONS: tRNA, rRNA and ncRNA genes emerged as the key genomic elements that underpin the classification of archaea and bacteria. In particular, higher nucleotide diversity was found in tRNA from bacteria compared to archaea. The analysis of the few classification errors reflects the complex phylogenetic relationships between bacteria, archaea and eukaryotes.},
}

*Archaea/genetics/classification
*Machine Learning
*Bacteria/genetics/classification
*Genomics/methods
*Genome, Archaeal
Genome, Bacterial
RNA, Transfer/genetics
Phylogeny

@article {pmid39390113,
year = {2024},
author = {Nagar, DN and Mani, K and Braganca, JM},
title = {Author Correction: Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcularubripromontorii BS2, Haloferaxlucentense BBK2 and Halogeometricumborinquense E3 isolated from the solar salterns of India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23750},
doi = {10.1038/s41598-024-74079-z},
pmid = {39390113},
issn = {2045-2322},
}

@article {pmid39383165,
year = {2024},
author = {, },
title = {Correction: A Versatile Medium for Cultivating Methanogenic Archaea.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0312093},
pmid = {39383165},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0061563.].},
}

@article {pmid39363002,
year = {2024},
author = {Mühling, L and Baur, T and Molitor, B},
title = {Methanothermobacter thermautotrophicus and Alternative Methanogens: Archaea-Based Production.},
journal = {Advances in biochemical engineering/biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39363002},
issn = {0724-6145},
abstract = {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.},
}

@article {pmid39360821,
year = {2024},
author = {Han, S and Kim, S and Sedlacek, CJ and Farooq, A and Song, C and Lee, S and Liu, S and Brüggemann, N and Rohe, L and Kwon, M and Rhee, S-K and Jung, M-Y},
title = {Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.},
journal = {mBio},
volume = {},
number = {},
pages = {e0216924},
doi = {10.1128/mbio.02169-24},
pmid = {39360821},
issn = {2150-7511},
abstract = {UNLABELLED: Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems.

IMPORTANCE: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.},
}

@article {pmid39359677,
year = {2024},
author = {Pereira, O and Qin, W and Galand, PE and Debroas, D and Lami, R and Hochart, C and Zhou, Y and Zhou, J and Zhang, C},
title = {Metabolic activities of marine ammonia-oxidizing archaea orchestrated by quorum sensing.},
journal = {mLife},
volume = {3},
number = {3},
pages = {417-429},
pmid = {39359677},
issn = {2770-100X},
abstract = {Ammonia-oxidizing archaea (AOA) play crucial roles in marine carbon and nitrogen cycles by fixing inorganic carbon and performing the initial step of nitrification. Evaluation of carbon and nitrogen metabolism popularly relies on functional genes such as amoA and accA. Increasing studies suggest that quorum sensing (QS) mainly studied in biofilms for bacteria may serve as a universal communication and regulatory mechanism among prokaryotes; however, this has yet to be demonstrated in marine planktonic archaea. To bridge this knowledge gap, we employed a combination of metabolic activity markers (amoA, accA, and grs) to elucidate the regulation of AOA-mediated nitrogen, carbon processes, and their interactions with the surrounding heterotrophic population. Through co-transcription investigations linking metabolic markers to potential key QS genes, we discovered that QS molecules could regulate AOA's carbon, nitrogen, and lipid metabolisms under different conditions. Interestingly, specific AOA ecotypes showed a preference for employing distinct QS systems and a distinct QS circuit involving a typical population. Overall, our data demonstrate that QS orchestrates nitrogen and carbon metabolism, including the exchange of organic metabolites between AOA and surrounding heterotrophic bacteria, which has been previously overlooked in marine AOA research.},
}

@article {pmid39348174,
year = {2024},
author = {Lehtovirta-Morley, LE and Ge, C and Ross, J and Yao, H and Hazard, C and Gubry-Rangin, C and Prosser, JI and Nicol, GW},
title = {Nitrosotalea devaniterrae gen. nov., sp. nov. and Nitrosotalea sinensis sp. nov., two acidophilic ammonia oxidising archaea isolated from acidic soil, and proposal of the new order Nitrosotaleales ord. nov. within the class Nitrososphaeria of the phylum Nitrososphaerota.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.006387},
pmid = {39348174},
issn = {1466-5034},
mesh = {*Soil Microbiology ; *Phylogeny ; *Base Composition ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Ammonia/metabolism ; *DNA, Archaeal/genetics ; *Oxidation-Reduction ; China ; Archaea/classification/genetics/isolation & purification ; Hydrogen-Ion Concentration ; Nitrites/metabolism ; Chemoautotrophic Growth ; },
abstract = {Two obligately acidophilic, mesophilic and aerobic soil ammonia-oxidising archaea were isolated from a pH 4.5 arable sandy loam (UK) and pH 4.7 acidic sulphate paddy soil (PR China) and designated strains Nd1[T] and Nd2[T], respectively. The strains shared more than 99 % 16S rRNA gene sequence identity and their genomes were both less than 2 Mb in length, sharing 79 % average nucleotide identity, 81 % average amino acid identity and a DNA G+C content of approximately 37 mol%. Both strains were chemolithotrophs that fixed carbon dioxide and gained energy by oxidising ammonia to nitrite, with no evidence of mixotrophic growth. Neither strain was capable of using urea as a source of ammonia. Both strains were non-motile in culture, although Nd1[T] does possess genes encoding flagella components and therefore may be motile under certain conditions. Cells of Nd1[T] were small angular rods 0.5-1 µm in length and grew at pH 4.2-5.6 and at 20-30 °C. Cells of Nd1[T] were small angular rods 0.5-1 µm in length and grew at pH 4.0-6.1 and at 20-42 °C. Nd1[T] and Nd2[T] are distinct with respect to genomic and physiological features and are assigned as the type strains for the species Nitrosotalea devaniterrae sp. nov. (type strain, Nd1[T]=NCIMB 15248[T]=DSM 110862[T]) and Nitrosotalea sinensis sp. nov. (type strain, Nd2[T]=NCIMB 15249[T]=DSM 110863[T]), respectively, within the genus Nitrosotalea gen. nov. The family Nitrosotaleaceae fam. nov. and order Nitrosotaleales ord. nov. are also proposed officially.},
}

*Soil Microbiology
*Phylogeny
*Base Composition
*RNA, Ribosomal, 16S/genetics
*Sequence Analysis, DNA
*Ammonia/metabolism
*DNA, Archaeal/genetics
*Oxidation-Reduction
China
Archaea/classification/genetics/isolation & purification
Hydrogen-Ion Concentration
Nitrites/metabolism
Chemoautotrophic Growth

@article {pmid39304533,
year = {2024},
author = {Zhang, QK and Zhu, LR and Dong, XY and Yang, XY and Hou, J and Cui, HL},
title = {Salinirarus marinus gen. nov., sp. nov., Haloplanus salilacus sp. nov., Haloplanus pelagicus sp. nov., Haloplanus halophilus sp. nov., Haloplanus halobius sp. nov., halophilic archaea isolated from commercial coarse salts with potential as starter cultures for salt-fermented foods.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae075},
pmid = {39304533},
issn = {1574-6968},
abstract = {Five halophilic archaeal strains, XH8T, CK5-1T, GDY1T, HW8-1T, and XH21T, were isolated from commercial coarse salt produced in different regions of China. Their 16S rRNA and rpoB' gene sequences indicated that four of the strains (CK5-1T, GDY1T, HW8-1T, and XH21T) represent distinct species within the genus Haloplanus (family Haloferacaceae), while strain XH8T represents a novel genus within the same family. These assignments were supported by phylogenetic and phylogenomic analyses, which showed that strains CK5-1T, GDY1T, HW8-1T, and XH21T cluster with the current species of the genus Haloplanus, while strain XH8T forms a separate branch from the genus Haloplanus. The digital DNA-DNA hybridization and average amino acid identity (AAI) values among these four strains and the current members of the genus Haloplanus were 23.1-35.2% and 75.9-83.8%, respectively; and those values between strain XH8T and other genera in the family Haloferacaceae were 18.8-33.6% and 59.8-66.6%, respectively, much lower than the threshold values for species demarcation. Strain XH8T may represent a novel genus of the family Haloferacaceae according to the cut-off value of AAI (≤72.1%) proposed to differentiate genera within the family Haloferacaceae. These five strains could be distinguished from the related species according to differential phenotypic characteristics. Based on these results, it is proposed that strain XH8T represents a novel genus within the family Haloferacaceae, and strains CK5-1T, GDY1T, HW8-1T, and XH21T represent four novel species of the genus Haloplanus, respectively. Additionally, these five strains possess genes encoding enzymes critical for the fermentation process in salt-fermented foods, indicating their potential as starter cultures for these applications.},
}

@article {pmid39300577,
year = {2024},
author = {Lezcano, MÁ and Bornemann, TLV and Sánchez-García, L and Carrizo, D and Adam, PS and Esser, SP and Cabrol, NA and Probst, AJ and Parro, V},
title = {Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {176},
pmid = {39300577},
issn = {2049-2618},
support = {FJC2018-037246-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC2018-023943-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC-2014-19446//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RTI2018-094368-B-I0//Spanish Ministry of Science and Innovation/State Agency of Research/ ; PEJD-2017- POST/TIC-4119//Spanish Ministry of Science and Innovation/State Agency of Research (EU Youth Employment Initiative)/ ; NAI-CAN7, 13NAI7_2-0018//NASA Astrobiology Institute/ ; DFG PR1603/2-1//German Research Foundation/ ; 161L0285E//German Federal Ministry of Education and Research/ ; },
mesh = {*Lakes/microbiology ; *Archaea/genetics/metabolism/classification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Genetic Variation ; Chile ; Phylogeny ; Microbiota ; Extremophiles/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile.

RESULTS: The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO4[2-]-S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and α- and γ-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota.

CONCLUSIONS: The high number of novel bacterial and archaeal MAGs in the Laguna Lejía indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.},
}

*Lakes/microbiology
*Archaea/genetics/metabolism/classification
*Geologic Sediments/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Genetic Variation
Chile
Phylogeny
Microbiota
Extremophiles/metabolism/genetics/classification
RNA, Ribosomal, 16S/genetics

@article {pmid39299940,
year = {2024},
author = {Obayori, OS and Salam, LB and Ashade, AO and Oseni, TD and Kalu, MD and Mustapha, FM},
title = {An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {10},
pages = {327},
pmid = {39299940},
issn = {1573-0972},
mesh = {*Metals, Heavy/analysis ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification/metabolism ; *Charcoal ; *Soil Pollutants/analysis ; *Soil/chemistry ; Nigeria ; High-Throughput Nucleotide Sequencing ; Animals ; Hydrocarbons/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.},
}

*Metals, Heavy/analysis
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification/metabolism
*Charcoal
*Soil Pollutants/analysis
*Soil/chemistry
Nigeria
High-Throughput Nucleotide Sequencing
Animals
Hydrocarbons/metabolism/analysis
RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid39296579,
year = {2024},
author = {Vershinin, Z and Zaretsky, M and Eichler, J},
title = {N-glycosylation in Archaea - Expanding the process, components and roles of a universal post-translational modification.},
journal = {BBA advances},
volume = {6},
number = {},
pages = {100120},
pmid = {39296579},
issn = {2667-1603},
abstract = {While performed by all three domains of life, N-glycosylation in Archaea is less well described than are the parallel eukaryal and bacterial processes. Still, what is known of the archaeal version of this universal post-translational modification reveals numerous seemingly domain-specific traits. Specifically, the biosynthesis of archaeal N-linked glycans relies on distinct pathway steps and components, rare sugars and sugar modifications, as well as unique lipid carriers upon which N-linked glycans are assembled. At the same time, Archaea possess the apparently unique ability to simultaneously modify their glycoproteins with very different N-linked glycans. In addition to these biochemical aspects of archaeal N-glycosylation, such post-translational modification has been found to serve a wide range of roles possibly unique to Archaea, including allowing these microorganisms to not only cope with the harsh physical conditions of the niches they can inhabit but also providing the ability to adapt to transient changes in such environments.},
}

@article {pmid39296305,
year = {2024},
author = {Hernández-Magaña, E and Kraft, B},
title = {Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1410251},
pmid = {39296305},
issn = {1664-302X},
abstract = {Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle and among the most abundant microorganisms in the ocean, thriving even in oxygen-depleted ecosystems. AOA produce the greenhouse gas nitrous oxide (N2O) as a byproduct of ammonia oxidation. Additionally, the recent discovery of a nitric oxide dismutation pathway in the AOA isolate Nitrosopumilus maritimus points toward other N2O production and consumption pathways in AOA. AOA that perform NO dismutation when exposed to oxygen depletion, produce oxygen and dinitrogen as final products. Based on the transient accumulation of N2O coupled with oxygen accumulation, N2O has been proposed as an intermediate in this novel archaeal pathway. In this study, we spiked N2O to oxygen-depleted incubations with pure cultures of two marine AOA isolates that were performing NO dismutation. By using combinations of N compounds with different isotopic signatures ([15]NO2 [-] pool +[44]N2O spike and [14]NO2 [-] pool +[46]N2O spike), we evaluated the N2O spike effects on the production of oxygen and the isotopic signature of N2 and N2O. The experiments confirmed that N2O is an intermediate in NO dismutation by AOA, distinguishing it from similar pathways in other microbial clades. Furthermore, we showed that AOA rapidly reduce high concentrations of spiked N2O to N2. These findings advance our understanding of microbial N2O production and consumption in oxygen-depleted settings and highlight AOA as potentially important key players in N2O turnover.},
}

@article {pmid39287442,
year = {2024},
author = {Mattick, JSA and Bromley, RE and Watson, KJ and Adkins, RS and Holt, CI and Lebov, JF and Sparklin, BC and Tyson, TS and Rasko, DA and Dunning Hotopp, JC},
title = {Deciphering transcript architectural complexity in bacteria and archaea.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0235924},
pmid = {39287442},
issn = {2150-7511},
abstract = {RNA transcripts are potential therapeutic targets, yet bacterial transcripts have uncharacterized biodiversity. We developed an algorithm for transcript prediction called tp.py using it to predict transcripts (mRNA and other RNAs) in Escherichia coli K12 and E2348/69 strains (Bacteria:gamma-Proteobacteria), Listeria monocytogenes strains Scott A and RO15 (Bacteria:Firmicute), Pseudomonas aeruginosa strains SG17M and NN2 strains (Bacteria:gamma-Proteobacteria), and Haloferax volcanii (Archaea:Halobacteria). From >5 million E. coli K12 and >3 million E. coli E2348/69 newly generated Oxford Nanopore Technologies direct RNA sequencing reads, 2,487 K12 mRNAs and 1,844 E2348/69 mRNAs were predicted, with the K12 mRNAs containing more than half of the predicted E. coli K12 proteins. While the number of predicted transcripts varied by strain based on the amount of sequence data used, across all strains examined, the predicted average size of the mRNAs was 1.6-1.7 kbp, while the median size of the 5'- and 3'-untranslated regions (UTRs) were 30-90 bp. Given the lack of bacterial and archaeal transcript annotation, most predictions were of novel transcripts, but we also predicted many previously characterized mRNAs and ncRNAs, including post-transcriptionally generated transcripts and small RNAs associated with pathogenesis in the E. coli E2348/69 LEE pathogenicity islands. We predicted small transcripts in the 100-200 bp range as well as >10 kbp transcripts for all strains, with the longest transcript for two of the seven strains being the nuo operon transcript, and for another two strains it was a phage/prophage transcript. This quick, easy, and reproducible method will facilitate the presentation of transcripts, and UTR predictions alongside coding sequences and protein predictions in bacterial genome annotation as important resources for the research community.IMPORTANCEOur understanding of bacterial and archaeal genes and genomes is largely focused on proteins since there have only been limited efforts to describe bacterial/archaeal RNA diversity. This contrasts with studies on the human genome, where transcripts were sequenced prior to the release of the human genome over two decades ago. We developed software for the quick, easy, and reproducible prediction of bacterial and archaeal transcripts from Oxford Nanopore Technologies direct RNA sequencing data. These predictions are urgently needed for more accurate studies examining bacterial/archaeal gene regulation, including regulation of virulence factors, and for the development of novel RNA-based therapeutics and diagnostics to combat bacterial pathogens, like those with extreme antimicrobial resistance.},
}

@article {pmid39281633,
year = {2024},
author = {Ben Hamad Bouhamed, S and Chaari, M and Baati, H and Zouari, S and Ammar, E},
title = {Extreme halophilic Archaea: Halobacterium salinarum carotenoids characterization and antioxidant properties.},
journal = {Heliyon},
volume = {10},
number = {17},
pages = {e36832},
pmid = {39281633},
issn = {2405-8440},
abstract = {Important marine microorganisms are resources of renewable energy that may face global population growth and needs. The application of biomass metabolites, such as carotenoids and their derivatives, may solve some agro-food health problems. Herein, a new halophilic Archaea Halobacterium salinarum producing carotenoid was screened from a Tunisian solar Saltworks (Sfax). The identification of the carotenoid pigments was carried out using HPLC-MS/MS. The predominant pigments produced by this Halobacterium were bacterioruberin and its derivatives and the carotenoids production was found to be of 21.51 mg/mL. Moreover, the data revealed that the carotenoids extract exhibited a high antioxidant activity across four oxidizing assays. The present results suggested that carotenoids extracted from halophilic Archaea are interesting sources of natural antioxidants for future innovative applications in agro-food, cosmetic and health fields.},
}

@article {pmid39215524,
year = {2024},
author = {Chatziargyri, AG and Stasi, EA and Tsirigos, KI and Litou, ZI and Iconomidou, VA and Bagos, PG},
title = {CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea.},
journal = {Journal of bioinformatics and computational biology},
volume = {22},
number = {4},
pages = {2450021},
doi = {10.1142/S0219720024500215},
pmid = {39215524},
issn = {1757-6334},
mesh = {*Protein Sorting Signals ; *Bacterial Proteins/metabolism/chemistry/genetics ; *Archaeal Proteins/metabolism/chemistry/genetics ; Archaea/metabolism/genetics ; Computational Biology/methods ; Cell Wall/metabolism/chemistry ; Markov Chains ; Amino Acid Motifs ; Software ; Bacteria/metabolism/genetics ; Algorithms ; },
abstract = {Sorting signals are crucial for the anchoring of proteins to the cell surface in archaea and bacteria. These proteins often feature distinct motifs at their C-terminus, cleaved by sortase or sortase-like enzymes. Gram-positive bacteria exhibit the LPXTGX consensus motif, cleaved by sortases, while Gram-negative bacteria employ exosortases recognizing motifs like PEP. Archaea utilize exosortase homologs known as archaeosortases for signal anchoring. Traditionally identification of such C-terminal sorting signals was performed with profile Hidden Markov Models (pHMMs). The Cell-Wall PREDiction (CW-PRED) method introduced for the first time a custom-made class HMM for proteins in Gram-positive bacteria that contain a cell wall sorting signal which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues. Here we present a new and updated version of CW-PRED for predicting C-terminal sorting signals in Archaea, Gram-positive, and Gram-negative bacteria. We used a large training set and several model enhancements that improve motif identification in order to achieve better discrimination between C-terminal signals and other proteins. Cross-validation demonstrates CW-PRED's superiority in sensitivity and specificity compared to other methods. Application of the method in reference proteomes reveals a large number of potential surface proteins not previously identified. The method is available for academic use at http://195.251.108.230/apps.compgen.org/CW-PRED/ and as standalone software.},
}

*Protein Sorting Signals
*Bacterial Proteins/metabolism/chemistry/genetics
*Archaeal Proteins/metabolism/chemistry/genetics
Archaea/metabolism/genetics
Computational Biology/methods
Cell Wall/metabolism/chemistry
Markov Chains
Amino Acid Motifs
Software
Bacteria/metabolism/genetics
Algorithms

@article {pmid39215388,
year = {2024},
author = {Tejedor-Sanz, S and Song, YE and Sundstrom, ER},
title = {Utilization of formic acid by extremely thermoacidophilic archaea species.},
journal = {Microbial biotechnology},
volume = {17},
number = {9},
pages = {e70003},
pmid = {39215388},
issn = {1751-7915},
support = {CW367480//Energy Biosciences Institute/ ; },
mesh = {*Formates/metabolism ; Sulfolobales/metabolism/genetics ; },
abstract = {The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO2, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1-2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.},
}

*Formates/metabolism
Sulfolobales/metabolism/genetics

@article {pmid39215047,
year = {2024},
author = {Nagar, DN and Mani, K and Braganca, JM},
title = {Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcula rubripromontorii BS2, Haloferax lucentense BBK2 and Halogeometricum borinquense E3 isolated from the solar salterns of India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20214},
pmid = {39215047},
issn = {2045-2322},
support = {(Level III) BT/INF/22/SP2543/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; 2023-24//DSTE&WM, Government of Goa/ ; },
mesh = {*Carotenoids/metabolism ; India ; *Phylogeny ; *Haloferax/genetics/metabolism ; *Haloarcula/genetics/metabolism ; Genome, Archaeal ; Whole Genome Sequencing ; RNA, Ribosomal, 16S/genetics ; Halobacteriaceae/genetics/metabolism/isolation & purification/classification ; Genomics/methods ; Base Composition ; },
abstract = {Haloarchaeal cultures were isolated from solar salterns of Goa and Tamil Nadu and designated as BS2, BBK2 and E3. These isolates grew with a characteristic bright orange to pink pigmentation and were capable of growing in media containing upto 25% (w/vol) NaCl. Whole genome sequencing (WGS) of the three haloarchaeal strains BS2, BBK2 and E3 indicated an assembled genomic size of 4.1 Mb, 3.8 Mb and 4 Mb with G + C content of 61.8, 65.6 and 59.8% respectively. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the archaeal isolates belong to Haloarcula, Haloferax and Halogeometricum genera. Haloarcula rubripromontorii BS2 was predicted to have 4292 genes with 4242 CDS regions, 46 tRNAs, 6 rRNAs and 3 misc_RNAs. In case of Haloferax lucentense BBK2,, 3840 genes with 3780 CDS regions were detected along with 52 tRNAs, 5 rRNAs and 3 misc_RNAs. Halogeometricum borinquense E3 contained 4101 genes, 4043 CDS regions, 52 tRNAs, 4 rRNAs, and 2 misc_RNAs. The functional annotation and curation of the haloarchaeal genome, revealed C50 carotenoid biosynthetic genes like phytoene desaturase/carotenoid 3' -4' desaturase (crtI), lycopene elongase (ubiA/lyeJ) and carotenoid biosynthesis membrane protein (cruF) in the three isolates. Whereas crtD (C-3',4' desaturase), crtY (lycopene cyclase) and brp/blh (β-carotene dioxygenase) genes were identified only in BS2.},
}

*Carotenoids/metabolism
India
*Phylogeny
*Haloferax/genetics/metabolism
*Haloarcula/genetics/metabolism
Genome, Archaeal
Whole Genome Sequencing
RNA, Ribosomal, 16S/genetics
Halobacteriaceae/genetics/metabolism/isolation & purification/classification
Genomics/methods
Base Composition

@article {pmid39210225,
year = {2024},
author = {da Costa Soares, S and Vezzani, FM and Favaretto, N and Auler, AC and da Silva Coelho, I and de Sousa Pires, A and Cruz, LM and de Souza, EM and Barth, G},
title = {Effect of long-term liquid dairy manure application on activity and structure of bacteria and archaea in no-till soils depends on plant in development.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {42},
pages = {54713-54728},
pmid = {39210225},
issn = {1614-7499},
mesh = {*Soil Microbiology ; *Manure/microbiology ; *Archaea ; *Bacteria ; *Soil/chemistry ; RNA, Ribosomal, 16S ; Brazil ; Agriculture/methods ; Dairying ; },
abstract = {This study aimed to evaluate the impact of long-term liquid dairy manure (LDM) application on the activity and structure of soil bacterial and archaea communities in two cropping seasons over 1 year of a no-till crop rotation system. The experiment was run in a sandy clay loam texture Oxisol, in Brazil, including LDM doses of 60, 120, and 180 m[3] ha[-1] year[-1], installed in 2005. Soil sampling was conducted during spring 2018 and autumn 2019 at 0-10-cm depth. Microbial biomass carbon and nitrogen, 16S rRNA gene sequencing, microbial respiration and quotient were performed. Over the 14-year period, LDM application increased soil microbial community activity. Analysis of 16S rRNA gene sequencing revealed dominance by Proteobacteria, Acidobacteria, and Actinobacteria phyla (67% in spring and 70% in autumn). Genera Pirulla and Nitrososphaera showed enrichment at LDM doses of 120 and 180 m[3] ha[-1] year[-1] doses, respectively. During spring, following black oat cropping, shifts in the relative abundance of Bacteroidetes, Proteobacteria, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Actinobacteria, and AD3 phyla were observed due to LDM application, correlating with soil chemical indicators such as pH, K, Ca, Mn, and Zn. Our findings indicate that plant development strongly influences microbial community composition, potentially outweighing the impact of LDM. Our findings indicate that the application of liquid dairy manure alters the soil bacterial activity and community; however, this effect depends on the developing plant.},
}

*Soil Microbiology
*Manure/microbiology
*Archaea
*Bacteria
*Soil/chemistry
RNA, Ribosomal, 16S
Brazil
Agriculture/methods
Dairying

@article {pmid39207169,
year = {2024},
author = {Baker, BJ and Sarno, N},
title = {Small archaea may form intimate partnerships to maximize their metabolic potential.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0034724},
pmid = {39207169},
issn = {2150-7511},
abstract = {DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024, https://doi.org/10.1128/mbio.02918-23). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N2O) reduction. However, N2O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N2O consumers) with other larger cells (N2O producers) demonstrates that N2O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes.},
}