@article {pmid36985129,
year = {2023},
author = {Slobodkin, AI and Ratnikova, NM and Slobodkina, GB and Klyukina, AA and Chernyh, NA and Merkel, AY},
title = {Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030555},
pmid = {36985129},
issn = {2076-2607},
abstract = {The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood-Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.},
}

@article {pmid36949474,
year = {2023},
author = {Regueira-Iglesias, A and Vázquez-González, L and Balsa-Castro, C and Vila-Blanco, N and Blanco-Pintos, T and Tamames, J and Carreira, MJ and Tomás, I},
title = {In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {58},
pmid = {36949474},
issn = {2049-2618},
mesh = {Humans ; *Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; DNA Primers/genetics ; Bacteria/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain.

RESULTS: A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) ≥75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively.

CONCLUSIONS: Given the three amplicon length categories (100-300, 301-600, and >600 base pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.},
}

Humans
*Archaea/genetics
RNA, Ribosomal, 16S/genetics
Genes, rRNA
DNA Primers/genetics
Bacteria/genetics
*Microbiota/genetics
High-Throughput Nucleotide Sequencing/methods
Phylogeny

@article {pmid36949220,
year = {2023},
author = {Lynes, MM and Krukenberg, V and Jay, ZJ and Kohtz, AJ and Gobrogge, CA and Spietz, RL and Hatzenpichler, R},
title = {Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {22},
pmid = {36949220},
issn = {2730-6151},
abstract = {Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.},
}

@article {pmid36927099,
year = {2023},
author = {Chen, J and Li, Y and Zhong, C and Xu, Z and Lu, G and Jing, H and Liu, H},
title = {Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117922},
doi = {10.1128/msystems.01179-22},
pmid = {36927099},
issn = {2379-5077},
abstract = {Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.},
}

@article {pmid36920214,
year = {2023},
author = {Adlung, N and Scheller, S},
title = {Application of the Fluorescence-Activating and Absorption-Shifting Tag (FAST) for Flow Cytometry in Methanogenic Archaea.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0178622},
doi = {10.1128/aem.01786-22},
pmid = {36920214},
issn = {1098-5336},
abstract = {Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans have been biochemically characterized and can be genetically engineered by using a variety of existing molecular tools. The anaerobic lifestyle and autofluorescence of methanogens, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives), which require oxygen for chromophore maturation. Recently, the use of a novel oxygen-independent fluorescent activation and absorption-shifting tag (FAST) was demonstrated with M. maripaludis. Similarly, we now describe the use of the tandem activation and absorption-shifting tag protein 2 (tdFAST2), which fluoresces when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. Expression of tdFAST2 in M. acetivorans and M. maripaludis is noncytotoxic and tdFAST2:HBR-3,5DOM fluorescence is clearly distinguishable from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be distinguished, thereby allowing for the possibility of high-throughput investigations of the characteristic dynamics within single and mixed cultures. IMPORTANCE Methane-producing archaea play an essential role in the global carbon cycle and demonstrate great potential for various biotechnological applications, e.g., biofuel production, carbon dioxide capture, and electrochemical systems. Oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins for studying methanogens. By using tdFAST2:HBR-3,5DOM fluorescence, which functions under anaerobic conditions and is distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of the mixed culture dynamics of methanogens via flow cytometry were made possible. This will further help accelerate the sustainable exploitation of methanogens.},
}

@article {pmid36912626,
year = {2023},
author = {Li, D and Ren, Z and Zhou, Y and Jiang, L and Zheng, M and Liu, G},
title = {Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0004723},
doi = {10.1128/aem.00047-23},
pmid = {36912626},
issn = {1098-5336},
abstract = {Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.},
}

@article {pmid36893867,
year = {2023},
author = {Cheng, H and Yang, Y and He, Y and Zhan, X and Liu, Y and Hu, Z and Huang, H and Yao, X and Yang, W and Jin, J and Ren, B and Liu, J and Hu, Q and Jin, Y and Shen, L},
title = {Spatio-temporal variations of activity of nitrate-driven anaerobic oxidation of methane and community structure of Candidatus Methanoperedens-like archaea in sediment of Wuxijiang river.},
journal = {Chemosphere},
volume = {324},
number = {},
pages = {138295},
doi = {10.1016/j.chemosphere.2023.138295},
pmid = {36893867},
issn = {1879-1298},
abstract = {Nitrate-driven anaerobic oxidation of methane (AOM), catalyzing by Candidatus Methanoperedens-like archaea, is a new addition in the global CH4 cycle. This AOM process acts as a novel pathway for CH4 emission reduction in freshwater aquatic ecosystems; however, its quantitative importance and regulatory factors in riverine ecosystems are nearly unknown. Here, we examined the spatio-temporal changes of the communities of Methanoperedens-like archaea and nitrate-driven AOM activity in sediment of Wuxijiang River, a mountainous river in China. These archaeal community composition varied significantly among reaches (upper, middle, and lower reaches) and between seasons (winter and summer), but their mcrA gene diversity showed no significant spatial or temporal variations. The copy numbers of Methanoperedens-like archaeal mcrA genes were 1.32 × 10[5]-2.47 × 10[7] copies g[-1] (dry weight), and the activity of nitrate-driven AOM was 0.25-1.73 nmol CH4 g[-1] (dry weight) d[-1], which could potentially reduce 10.3% of CH4 emissions from rivers. Significant spatio-temporal variations of mcrA gene abundance and nitrate-driven AOM activity were found. Both the gene abundance and activity increased significantly from upper to lower reaches in both seasons, and were significantly higher in sediment collected in summer than in winter. In addition, the variations of Methanoperedens-like archaeal communities and nitrate-driven AOM activity were largely impacted by the sediment temperature, NH4[+] and organic carbon contents. Taken together, both time and space scales need to be considered for better evaluating the quantitative importance of nitrate-driven AOM in reducing CH4 emissions from riverine ecosystems.},
}

@article {pmid36888658,
year = {2023},
author = {Wan, XS and Hou, L and Kao, SJ and Zhang, Y and Sheng, HX and Shen, H and Tong, S and Qin, W and Ward, BB},
title = {Pathways of N2O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {11},
pages = {e2220697120},
doi = {10.1073/pnas.2220697120},
pmid = {36888658},
issn = {1091-6490},
abstract = {The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N2O), to the atmosphere. Most of that N2O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N2O production and their kinetics, however, are not completely understood. Here, we use [15]N and [18]O isotopes to determine the kinetics of N2O production and trace the source of nitrogen (N) and oxygen (O) atoms in N2O produced by a model marine AOA species, Nitrosopumilus maritimus. We find that during ammonia oxidation, the apparent half saturation constants of nitrite and N2O production are comparable, suggesting that both processes are enzymatically controlled and tightly coupled at low ammonia concentrations. The constituent atoms in N2O are derived from ammonia, nitrite, O2, and H2O via multiple pathways. Ammonia is the primary source of N atoms in N2O, but its contribution varies with ammonia to nitrite ratio. The ratio of [45]N2O to [46]N2O (i.e., single or double labeled N) varies with substrate ratio, leading to widely varying isotopic signatures in the N2O pool. O2 is the primary source for O atoms. In addition to the previously demonstrated hybrid formation pathway, we found a substantial contribution by hydroxylamine oxidation, while nitrite reduction is an insignificant source of N2O. Our study highlights the power of dual [15]N-[18]O isotope labeling to disentangle N2O production pathways in microbes, with implications for interpretation of pathways and regulation of marine N2O sources.},
}

@article {pmid36880756,
year = {2023},
author = {Taubner, RS and Baumann, LMF and Steiner, M and Pfeifer, K and Reischl, B and Korynt, K and Bauersachs, T and Mähnert, B and Clifford, EL and Peckmann, J and Schuster, B and Birgel, D and Rittmann, SKR},
title = {Lipidomics and Comparative Metabolite Excretion Analysis of Methanogenic Archaea Reveal Organism-Specific Adaptations to Varying Temperatures and Substrate Concentrations.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0115922},
doi = {10.1128/msystems.01159-22},
pmid = {36880756},
issn = {2379-5077},
abstract = {Methanogenic archaea possess diverse metabolic characteristics and are an ecologically and biotechnologically important group of anaerobic microorganisms. Although the scientific and biotechnological value of methanogens is evident with regard to their methane-producing physiology, little is known about their amino acid excretion, and virtually nothing is known about the lipidome at different substrate concentrations and temperatures on a quantitative comparative basis. Here, we present the lipidome and a comprehensive quantitative analysis of proteinogenic amino acid excretion as well as methane, water, and biomass production of the three autotrophic, hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanothermococcus okinawensis, and Methanocaldococcus villosus under varying temperatures and nutrient supplies. The patterns and rates of production of excreted amino acids and the lipidome are unique for each tested methanogen and can be modulated by varying the incubation temperature and substrate concentration, respectively. Furthermore, the temperature had a significant influence on the lipidomes of the different archaea. The water production rate was much higher, as anticipated from the rate of methane production for all studied methanogens. Our results demonstrate the need for quantitative comparative physiological studies connecting intracellular and extracellular constraints of organisms to holistically investigate microbial responses to environmental conditions. IMPORTANCE Biological methane production by methanogenic archaea has been well studied for biotechnological purposes. This study reveals that methanogenic archaea actively modulate their lipid inventory and proteinogenic amino acid excretion pattern in response to environmental changes and the possible utilization of methanogenic archaea as microbial cell factories for the targeted production of lipids and amino acids.},
}

@article {pmid36874274,
year = {2023},
author = {Mei, R and Kaneko, M and Imachi, H and Nobu, MK},
title = {The origin and evolution of methanogenesis and Archaea are intertwined.},
journal = {PNAS nexus},
volume = {2},
number = {2},
pages = {pgad023},
pmid = {36874274},
issn = {2752-6542},
abstract = {Methanogenesis has been widely accepted as an ancient metabolism, but the precise evolutionary trajectory remains hotly debated. Disparate theories exist regarding its emergence time, ancestral form, and relationship with homologous metabolisms. Here, we report the phylogenies of anabolism-involved proteins responsible for cofactor biosynthesis, providing new evidence for the antiquity of methanogenesis. Revisiting the phylogenies of key catabolism-involved proteins further suggests that the last Archaea common ancestor (LACA) was capable of versatile H2-, CO2-, and methanol-utilizing methanogenesis. Based on phylogenetic analyses of the methyl/alkyl-S-CoM reductase family, we propose that, in contrast to current paradigms, substrate-specific functions emerged through parallel evolution traced back to a nonspecific ancestor, which likely originated from protein-free reactions as predicted from autocatalytic experiments using cofactor F430. After LACA, inheritance/loss/innovation centered around methanogenic lithoautotrophy coincided with ancient lifestyle divergence, which is clearly reflected by genomically predicted physiologies of extant archaea. Thus, methanogenesis is not only a hallmark metabolism of Archaea, but the key to resolve the enigmatic lifestyle that ancestral archaea took and the transition that led to physiologies prominent today.},
}

@article {pmid36842598,
year = {2023},
author = {Zheng, P and Zhang, Q and Zou, J and Han, Q and Han, J and Wang, Q and Yao, L and Yu, G and Liang, Y},
title = {A new strategy for the enrichment of ammonia-oxidizing archaea in wastewater treatment systems: The positive role of quorum-sensing signaling molecules.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {162385},
doi = {10.1016/j.scitotenv.2023.162385},
pmid = {36842598},
issn = {1879-1026},
abstract = {Ammonia-oxidizing archaea (AOA) play an important role in natural nitrogen cycle, but are difficult to be enriched in wastewater treatment systems. In this experiment, under ambient temperature and high dissolved oxygen, different types of acyl-homoserine lactones (C6-HSL, C8-HSL, C10-HSL, C14-HSL and 3-oxo-C14-HSL) were added to five wastewater nitrification systems to achieve AOA enrichment. Results showed that AOA couldn't be detected in the blank group without the addition of signaling molecules, while the AOA could be detected in all the reactors with the addition. The enrichment effect of AOA was not obvious with added 100 or 200 nmol/L signaling molecules, while the enrichment effect was both obvious with added C8-HSL of 400 nmol/L and C10-HSL of 800 nmol/L. And relative abundance of AOA increased from undetected in the control group to 1.10 % and 0.96 %, respectively. The exogenous signaling molecules may provide new view for AOA enrichment in wastewater treatment systems.},
}

@article {pmid36835573,
year = {2023},
author = {Ngcobo, PE and Nkosi, BVZ and Chen, W and Nelson, DR and Syed, K},
title = {Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
pmid = {36835573},
issn = {1422-0067},
abstract = {Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study's results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.},
}

@article {pmid36817958,
year = {2023},
author = {Kisly, I and Tamm, T},
title = {Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {1249-1261},
pmid = {36817958},
issn = {2001-0370},
abstract = {In three domains of life, proteins are synthesized by large ribonucleoprotein particles called ribosomes. All ribosomes are composed of ribosomal RNAs (rRNA) and numerous ribosomal proteins (r-protein). The three-dimensional shape of ribosomes is mainly defined by a tertiary structure of rRNAs. In addition, rRNAs have a major role in decoding the information carried by messenger RNAs and catalyzing the peptide bond formation. R-proteins are essential for shaping the network of interactions that contribute to a various aspects of the protein synthesis machinery, including assembly of ribosomes and interaction of ribosomal subunits. Structural studies have revealed that many key components of ribosomes are conserved in all life domains. Besides the core structure, ribosomes contain domain-specific structural features that include additional r-proteins and extensions of rRNA and r-proteins. This review focuses specifically on those r-proteins that are found only in archaeal and eukaryotic ribosomes. The role of these archaea/eukaryote specific r-proteins in stabilizing the ribosome structure is discussed. Several examples illustrate their functions in the formation of the internal network of ribosomal subunits and interactions between the ribosomal subunits. In addition, the significance of these r-proteins in ribosome biogenesis and protein synthesis is highlighted.},
}

@article {pmid36815558,
year = {2023},
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 meetings held 24 September 2020 and 8 October 2020.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.005775},
pmid = {36815558},
issn = {1466-5034},
}

@article {pmid36814573,
year = {2023},
author = {Cheng, X and Xiang, X and Yun, Y and Wang, W and Wang, H and Bodelier, PLE},
title = {Archaea and their interactions with bacteria in a karst ecosystem.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1068595},
pmid = {36814573},
issn = {1664-302X},
abstract = {Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 [+] availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca[2+], and NO2 [-]. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.},
}

@article {pmid36808147,
year = {2023},
author = {Gios, E and Mosley, OE and Weaver, L and Close, M and Daughney, C and Handley, KM},
title = {Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {13},
pmid = {36808147},
issn = {2730-6151},
abstract = {Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.},
}

@article {pmid36804975,
year = {2023},
author = {Zhang, Q and Chen, M and Leng, Y and Wang, X and Fu, Y and Wang, D and Zhao, X and Gao, W and Li, N and Chen, X and Fan, C and Li, Q},
title = {Organic substitution stimulates ammonia oxidation-driven N2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {162183},
doi = {10.1016/j.scitotenv.2023.162183},
pmid = {36804975},
issn = {1879-1026},
abstract = {Partial organic substitution (POS) is pivotal in enhancing soil productivity and changing nitrous oxide (N2O) emissions by profoundly altering soil nitrogen (N) cycling, where ammonia oxidation is a fundamental core process. However, the regulatory mechanisms of N2O production by ammonia oxidizers at the microbial community level under POS regimes remain unclear. This study explored soil ammonia oxidation and related N2O production, further building an understanding of the correlations between ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) activity and community structure in tropical arable soils under four-year field management regimes (CK, without fertilizer N; N, with only inorganic N; M1N1, with 1/2 organic N + 1/2 inorganic N; M1N2, with 1/3 organic N + 2/3 inorganic N). AOA contributed more to potential ammonia oxidation (PAO) than AOB across all treatments. In comparison with CK, N treatment had no obvious effects on PAO and lowered related N2O emissions by decreasing soil pH and downregulating the abundance of AOA- and AOB-amoA. POS regimes significantly enhanced PAO and N2O emissions relative to N treatment by promoting the abundances and contributions of AOA and AOB. The stimulated AOA-dominated N2O production under M1N1 was correlated with promoted development of Nitrososphaera. By contrast, the increased AOB-dominated N2O production under M1N2 was linked to the enhanced development of Nitrosospira multiformis. Our study suggests organic substitutions with different proportions of inorganic and organic N distinctively regulate the development of specific species of ammonia oxidizers to increase associated N2O emissions. Accordingly, appropriate options should be adopted to reduce environmental risks under POS regimes in tropical croplands.},
}

@article {pmid36796795,
year = {2023},
author = {Diao, M and Balkema, C and Muñoz, MS and Huisman, J and Muyzer, G},
title = {Succession of bacteria and archaea involved in the nitrogen cycle of a seasonally stratified lake.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnad013},
pmid = {36796795},
issn = {1574-6968},
abstract = {Human-driven changes affect nutrient inputs, oxygen solubility and the hydrodynamics of lakes, which affect biogeochemical cycles mediated by microbial communities. However, information on the succession of microbes involved in nitrogen cycling in seasonally stratified lakes is still incomplete. Here, we investigated the succession of nitrogen-transforming microorganisms in Lake Vechten over 19 months, combining 16S rRNA gene amplicon sequencing and quantification of functional genes. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) and anammox bacteria were abundant in the sediment during winter, accompanied by nitrate in the water column. Nitrogen-fixing bacteria and denitrifying bacteria emerged in the water column in spring when nitrate was gradually depleted. Denitrifying bacteria containing nirS genes were exclusively present in the anoxic hypolimnion. During summer stratification, abundances of AOA, AOB and anammox bacteria decreased sharply in the sediment, and ammonium accumulated in hypolimnion. After lake mixing during fall turnover, abundances of AOA, AOB and anammox bacteria increased and ammonium was oxidized to nitrate. Hence, nitrogen-transforming microorganisms in Lake Vechten displayed a pronounced seasonal succession, which was strongly determined by the seasonal stratification pattern. These results imply that changes in stratification and vertical mixing induced by global warming are likely to alter the nitrogen cycle of seasonally stratified lakes.},
}

@article {pmid36794928,
year = {2023},
author = {Akpudo, YM and Bezuidt, OK and Makhalanyane, TP},
title = {Metagenome-Assembled Genomes of Four Southern Ocean Archaea Harbor Multiple Genes Linked to Polyethylene Terephthalate and Polyhydroxybutyrate Plastic Degradation.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0109822},
doi = {10.1128/mra.01098-22},
pmid = {36794928},
issn = {2576-098X},
abstract = {Here, we present four archaeal metagenome-assembled genomes (MAGs) (three Thaumarchaeota MAGs and one Thermoplasmatota MAG) from a polar upwelling zone in the Southern Ocean. These archaea harbor putative genes encoding enzymes such as polyethylene terephthalate (PET) hydrolases (PETases) and polyhydroxybutyrate (PHB) depolymerases, which are associated with microbial degradation of PET and PHB plastics.},
}

@article {pmid36792581,
year = {2023},
author = {Filée, J and Becker, HF and Mellottee, L and Eddine, RZ and Li, Z and Yin, W and Lambry, JC and Liebl, U and Myllykallio, H},
title = {Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {838},
pmid = {36792581},
issn = {2041-1723},
abstract = {Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.},
}

@article {pmid36782524,
year = {2023},
author = {Beltran, L and Cvirkaite-Krupovic, V and Roberts, J and Wang, F and Kreutzberger, MA and Costa, T and Levental, I and Conticello, V and Egelman, EH and Krupovic, M},
title = {Domesticated conjugation machinery promotes DNA exchange in hyperthermophilic archaea.},
journal = {Biophysical journal},
volume = {122},
number = {3S1},
pages = {11a},
doi = {10.1016/j.bpj.2022.11.291},
pmid = {36782524},
issn = {1542-0086},
}

@article {pmid36759127,
year = {2023},
author = {Wolff, P and Lechner, A and Droogmans, L and Grosjean, H and Westhof, E},
title = {Identification of Up47 in three thermophilic archaea, one mesophilic archaeon and one hyperthermophilic bacterium.},
journal = {RNA (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1261/rna.079546.122},
pmid = {36759127},
issn = {1469-9001},
abstract = {Analysis of tRNA modifications profile in several Archaea allowed to observe a novel modified uridine in the V-loop of several tRNAs from two species: Pyrococcus furiosus and Sulfolobus acidocaldarius (Wolff et al. 2020). Recently, Ohira et al. (Ohira et al. 2022) characterized 2'-phosphouridine (Up) at position 47 in tRNAs of thermophilic Sulfurisphaera tokodaii, as well as in several other archaea and thermophilic bacteria. From the presence of the gene arkI corresponding to the RNA kinase responsible for Up47 formation, they also concluded that Up47 should be present in tRNAs of other thermophilic Archaea. Re-analysis of our earlier data confirms that the unidentified residue in tRNAs of both P. furiosus and S. acidocaldarius is indeed 2'phosphouridine followed by m5C48. Moreover, we find this modification in several tRNAs of other Archaea and of the hyperthermophilic bacterium Aquifex aeolicus.},
}

@article {pmid36752722,
year = {2023},
author = {Cooper, CR and Lewis, AM and Notey, JS and Mukherjee, A and Willard, DJ and Blum, PH and Kelly, RM},
title = {Interplay between Transcriptional Regulators and VapBC Toxin-Antitoxin Loci During Thermal Stress Response in Extremely Thermoacidophilic Archaea.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16350},
pmid = {36752722},
issn = {1462-2920},
abstract = {Thermoacidophilic archaea lack sigma factors and the large inventory of heat shock proteins (HSP) widespread in bacterial genomes, suggesting other strategies for handling thermal stress are involved. Heat shock transcriptomes for the thermoacidophilic archaeon Saccharolobus (f. Sulfolobus) solfataricus 98/2 revealed genes that were highly responsive to thermal stress, including transcriptional regulators YtrASs (Ssol_2420) and FadRSs (Ssol_0314), as well as Type II Toxin-Antitoxin (TA) loci VapBC6 (Ssol_2337, Ssol_2338) and VapBC22 (Ssol_0819, Ssol_0818). The role, if any, of Type II TA loci during stress response in microorganisms, such as Escherichia coli, is controversial. But, when genes encoding YtrASs , FadRSs , VapC22, VapB6, and VapC6 were systematically mutated in Sa. solfataricus 98/2, significant up-regulation of the other genes within this set was observed, implicating an interconnected regulatory network during thermal stress response. VapBC6 and VapBC22 have close homologs in other Sulfolobales, as well as in other archaea (e.g., Pyrococcus furiosus and Archaeoglobus fulgidus), and their corresponding genes were also heat shock responsive. The interplay between VapBC TA loci and heat shock regulators in Sa. solfataricus 98/2 not only indicates a cellular mechanism for heat shock response that differs from bacteria but one that could have common features within the thermophilic archaea. This article is protected by copyright. All rights reserved.},
}

@article {pmid36752534,
year = {2023},
author = {Borg Dahl, M and Kreyling, J and Petters, S and Wang, H and Mortensen, MS and Maccario, L and Sørensen, SJ and Urich, T and Weigel, R},
title = {Warmer winters result in reshaping of the European beech forest soil microbiome (bacteria, archaea and fungi) - with potential implications for ecosystem functioning.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16347},
pmid = {36752534},
issn = {1462-2920},
abstract = {In temperate regions climate warming alters temperature and precipitation regimes. During winter, a decline in insulating snow cover changes the soil environment, where especially frost exposure can have severe implications for soil microorganisms and subsequently for soil nutrient dynamics. Here we investigated winter climate change responses in European beech forests soil microbiome. Nine study sites with each three treatments (snow exclusion, insolation, and ambient) were investigated. Long-term adaptation to average climate was explored by comparing across sites. Triplicated treatment plots were used to evaluate short-term (one single winter) responses. Community profiles of bacteria, archaea and fungi were created using amplicon sequencing. Correlation between the microbiome, vegetation and soil physicochemical properties were found. We identify core members of the forest-microbiome, and link them to key processes e.g. mycorrhizal symbiont and specialized beech wood degraders (fungi) and nitrogen cycling (bacteria, archaea). For bacteria, the shift of the microbiome composition due to short-term soil temperature manipulations in winter was similar to the community differences observed between long-term relatively cold to warm conditions. The results suggest a strong link between the changes in the microbiomes and changes in environmental processes, e.g. nitrogen dynamics, driven by variation in winter climate. This article is protected by copyright. All rights reserved.},
}

@article {pmid36729913,
year = {2023},
author = {Denise, R and Babor, J and Gerlt, JA and de Crécy-Lagard, V},
title = {Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.},
journal = {Microbial genomics},
volume = {9},
number = {2},
pages = {},
doi = {10.1099/mgen.0.000926},
pmid = {36729913},
issn = {2057-5858},
}

@article {pmid36724220,
year = {2023},
author = {Ngugi, DK and Salcher, MM and Andrei, AS and Ghai, R and Klotz, F and Chiriac, MC and Ionescu, D and Büsing, P and Grossart, HP and Xing, P and Priscu, JC and Alymkulov, S and Pester, M},
title = {Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.},
journal = {Science advances},
volume = {9},
number = {5},
pages = {eadc9392},
doi = {10.1126/sciadv.adc9392},
pmid = {36724220},
issn = {2375-2548},
abstract = {Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.},
}

@article {pmid36721520,
year = {2022},
author = {Beddal, A and Boutaiba, S and Laassami, A and Hamaidi, F and Enache, M},
title = {Characterization by polyphasic approach of some indigenous halophilic archaea of Djelfa's rock salt "Hadjr el Meelh", Algeria.},
journal = {Iranian journal of microbiology},
volume = {14},
number = {4},
pages = {535-544},
pmid = {36721520},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Hadjr El Melh of Djelfa is an example of hypersaline ecosystems, which can harbor a wide variety of microorganisms under hostile physicochemical conditions. Given the importance of the study of halophilic microorganisms present there in terms of fundamental and applied microbiology, the purpose of this study was to characterize some halophilic archaea isolated from the brines of this environment.

MATERIALS AND METHODS: Eight water samples were chosen randomly and collected for physicochemical and microbiological analyses. Isolation of halophilic archaea was carried out by membrane filter technique. Ten strains were identified by polyphasic approach and tested for enzymes production.

RESULTS: Water samples of Djelfa's rock salt were slightly acidic to neutral in pH (6.55-7.36) with salinity ranging from 258.68 g/l to 493.91 g/l. Phenotypic, biochemical, taxonomic and phylogenetic characteristics indicated that all strains were classified within the family of Halobacteiaceae. Based on the comparison of DNA sequences encoded 16S rRNA, it was determined that seven strains were affiliated to the genus Haloarcula, two strains were related to the genus Halobacterium and one strain within the genus Haloferax. Production of different enzymes such as protease, amylase, esterase, lipase, lecithinase, gelatinase and cellulase on solid medium indicated that one strain (S2-2) produced amylase, esterase, lecithinase and protease. However, no strains showed cellulolytic or lipolytic activity. Gelatinase was found in all tested strains.

CONCLUSION: This report constitutes the first preliminary study of culturable halophilic archaea recovered from the brines of Djelfa's rock salt with a promising enzymatic potential in various fields of biotechnology.},
}

@article {pmid36721060,
year = {2023},
author = {Hodgskiss, LH and Melcher, M and Kerou, M and Chen, W and Ponce-Toledo, RI and Savvides, SN and Wienkoop, S and Hartl, M and Schleper, C},
title = {Unexpected complexity of the ammonia monooxygenase in archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36721060},
issn = {1751-7370},
abstract = {Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.},
}

@article {pmid36720870,
year = {2023},
author = {Daugeron, MC and Missoury, S and Da Cunha, V and Lazar, N and Collinet, B and van Tilbeurgh, H and Basta, T},
title = {A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {526},
doi = {10.1038/s41467-023-36210-y},
pmid = {36720870},
issn = {2041-1723},
abstract = {In Archaea and Eukaryotes, the synthesis of a universal tRNA modification, N[6]-threonyl-carbamoyl adenosine (t[6]A), is catalyzed by the KEOPS complex composed of Kae1, Bud32, Cgi121, and Pcc1. A fifth subunit, Gon7, is found only in Fungi and Metazoa. Here, we identify and characterize a fifth KEOPS subunit in Archaea. This protein, dubbed Pcc2, is a paralog of Pcc1 and is widely conserved in Archaea. Pcc1 and Pcc2 form a heterodimer in solution, and show modest sequence conservation but very high structural similarity. The five-subunit archaeal KEOPS does not form dimers but retains robust tRNA binding and t[6]A synthetic activity. Pcc2 can substitute for Pcc1 but the resulting KEOPS complex is inactive, suggesting a distinct function for the two paralogs. Comparative sequence and structure analyses point to a possible evolutionary link between archaeal Pcc2 and eukaryotic Gon7. Our work indicates that Pcc2 regulates the oligomeric state of the KEOPS complex, a feature that seems to be conserved from Archaea to Eukaryotes.},
}

@article {pmid36715325,
year = {2023},
author = {Yang, Y and Liu, J and Fu, X and Zhou, F and Zhang, S and Zhang, X and Huang, Q and Krupovic, M and She, Q and Ni, J and Shen, Y},
title = {A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad006},
pmid = {36715325},
issn = {1362-4962},
abstract = {Cell cycle regulation is of paramount importance for all forms of life. Here, we report that a conserved and essential cell cycle-specific transcription factor (designated as aCcr1) and its viral homologs control cell division in Sulfolobales. We show that the transcription level of accr1 reaches peak during active cell division (D-phase) subsequent to the expression of CdvA, an archaea-specific cell division protein. Cells over-expressing the 58-aa-long RHH (ribbon-helix-helix) family cellular transcription factor as well as the homologs encoded by large spindle-shaped viruses Acidianus two-tailed virus (ATV) and Sulfolobus monocaudavirus 3 (SMV3) display significant growth retardation and cell division failure, manifesting as enlarged cells with multiple chromosomes. aCcr1 over-expression results in downregulation of 17 genes (>4-fold), including cdvA. A conserved motif, aCcr1-box, located between the TATA-binding box and the translation initiation site of 13 out of the 17 highly repressed genes, is critical for aCcr1 binding. The aCcr1-box is present in the promoters and 5' UTRs of cdvA genes across Sulfolobales, suggesting that aCcr1-mediated cdvA repression is an evolutionarily conserved mechanism by which archaeal cells dictate cytokinesis progression, whereas their viruses take advantage of this mechanism to manipulate the host cell cycle.},
}

@article {pmid36709544,
year = {2023},
author = {Umegawa, Y and Kawatake, S and Murata, M and Matsuoka, S},
title = {Combined effect of the head groups and alkyl chains of archaea lipids when interacting with bacteriorhodopsin.},
journal = {Biophysical chemistry},
volume = {294},
number = {},
pages = {106959},
doi = {10.1016/j.bpc.2023.106959},
pmid = {36709544},
issn = {1873-4200},
abstract = {Bacteriorhodopsin (bR), a transmembrane protein with seven α-helices, is highly expressed in the purple membrane (PM) of archaea such as Halobacterium salinarum. It is well known that bR forms two-dimensional crystals with acidic lipids such as phosphatidylglycerol phosphate methyl ester (PGP-Me)-a major component of PM lipids bearing unique chemical structures-methyl-branched alkyl chains, ether linkages, and divalent anionic head groups with two phosphodiester groups. Therefore, we aimed to determine which functional groups of PGP-Me are essential for the boundary lipids of bR and how these functionalities interact with bR. To this end, we compared various well-known phospholipids (PLs) that carry one of the structural features of PGP-Me, and evaluated the affinity of PLs to bR using the centerband-only analysis of rotor-unsynchronized spin echo (COARSE) method in solid-state NMR measurements and thermal shift assays. The results clearly showed that the branched methyl groups of alkyl chains and double negative charges in the head groups are important for PL interactions with bR. We then examined the effect of phospholipids on the monomer-trimer exchange of bR using circular dichroism (CD) spectra. The results indicated that the divalent negative charge in a head group stabilizes the trimer structure, while the branched methyl chains significantly enhance the PLs' affinity for bR, thus dispersing bR trimers in the PM even at high concentrations. Finally, we investigated the effects of PL on the proton-pumping activity of bR based on the decay rate constant of the M intermediate of a bR photocycle. The findings showed that bR activities decreased to 20% in 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA), and in 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) bilayers as compared to that in PM. Meanwhile, 1,2-Diphytanoyl-sn-glycero-3-phosphate (DPhPA) bilayers bearing both negative charges and branched methyl groups preserved over 80% of the activity. These results strongly suggest that the head groups and alkyl chains of phospholipids are essential for boundary lipids and greatly influence the biological function of bR.},
}

@article {pmid36697601,
year = {2021},
author = {Sumi, T and Harada, K},
title = {Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea.},
journal = {Communications chemistry},
volume = {4},
number = {1},
pages = {149},
pmid = {36697601},
issn = {2399-3669},
abstract = {The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood-Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.},
}

@article {pmid36694212,
year = {2023},
author = {Jaffe, AL and Bardot, C and Le Jeune, AH and Liu, J and Colombet, J and Perrière, F and Billard, H and Castelle, CJ and Lehours, AC and Banfield, JF},
title = {Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {14},
pmid = {36694212},
issn = {2049-2618},
abstract = {BACKGROUND: Permanently stratified lakes contain diverse microbial communities that vary with depth and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined.

RESULTS: Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that the oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. On the whole, though, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments.

CONCLUSIONS: Overall, our analyses suggest that environmental gradients in Lac Pavin select for capacities of CPR bacteria and phages to a lesser extent than for other bacteria and archaea. This may be due to the fact that selection in the former groups is indirect and depends primarily on host characteristics. Video Abstract.},
}

@article {pmid36690779,
year = {2023},
author = {Yu, Y and Wang, P and Cao, HY and Teng, ZJ and Zhu, Y and Wang, M and McMinn, A and Chen, Y and Xiang, H and Zhang, YZ and Chen, XL and Zhang, YQ},
title = {Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36690779},
issn = {1751-7370},
abstract = {D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.},
}

@article {pmid36687602,
year = {2022},
author = {Corona Ramírez, A and Cailleau, G and Fatton, M and Dorador, C and Junier, P},
title = {Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {826117},
pmid = {36687602},
issn = {1664-302X},
abstract = {The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.},
}

@article {pmid36683362,
year = {2022},
author = {Tandon, K and Ricci, F and Costa, J and Medina, M and Kühl, M and Blackall, LL and Verbruggen, H},
title = {Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera.},
journal = {GigaScience},
volume = {12},
number = {},
pages = {},
doi = {10.1093/gigascience/giac127},
pmid = {36683362},
issn = {2047-217X},
abstract = {At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.},
}

@article {pmid36674956,
year = {2023},
author = {Baehren, C and Pembaur, A and Weil, PP and Wewers, N and Schult, F and Wirth, S and Postberg, J and Aydin, M},
title = {The Overlooked Microbiome-Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes.},
journal = {International journal of molecular sciences},
volume = {24},
number = {2},
pages = {},
doi = {10.3390/ijms24021426},
pmid = {36674956},
issn = {1422-0067},
abstract = {In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the relevance of archaea in human health and diseases. Contemporary broad availability and spread of next generation sequencing techniques now enable a stronger focus on such microorganisms, whose cultivation is difficult. However, due to the enormous evolutionary distances between bacteria, archaea and eukaryotes, the implementation of sequencing strategies for smaller laboratory scales needs to be refined to achieve as a holistic view on the microbiome as possible. Here, we present a technical approach that enables simultaneous analyses of archaeal, bacterial and eukaryotic microbial communities to study their roles in development and courses of respiratory disorders. We thus applied combinatorial 16S-/18S-rDNA sequencing strategies for sequencing-library preparation. Considering the lower total microbiota density of airway surfaces, when compared with gut microbiota, we optimized the DNA purification workflow from nasopharyngeal swab specimens. As a result, we provide a protocol that allows the efficient combination of bacterial, archaeal, and eukaryotic libraries for nanopore-sequencing using Oxford Nanopore Technologies MinION devices and subsequent phylogenetic analyses. In a pilot study, this workflow allowed the identification of some environmental archaea, which were not correlated with airway microbial communities before. Moreover, we assessed the protocol's broader applicability using a set of human stool samples. We conclude that the proposed protocol provides a versatile and adaptable tool for combinatorial studies on bacterial, archaeal, and eukaryotic microbiomes on a small laboratory scale.},
}

@article {pmid36671499,
year = {2023},
author = {De Lise, F and Iacono, R and Moracci, M and Strazzulli, A and Cobucci-Ponzano, B},
title = {Archaea as a Model System for Molecular Biology and Biotechnology.},
journal = {Biomolecules},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/biom13010114},
pmid = {36671499},
issn = {2218-273X},
abstract = {Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.},
}

@article {pmid36660825,
year = {2023},
author = {Nissley, AJ and Penev, PI and Watson, ZL and Banfield, JF and Cate, JHD},
title = {Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkac1273},
pmid = {36660825},
issn = {1362-4962},
support = {T32 066698/GF/NIH HHS/United States ; },
abstract = {The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3'-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.},
}

@article {pmid36659324,
year = {2017},
author = {Feng, Y and Dolfing, J and Guo, Z and Zhang, J and Zhang, G and Li, S and Lin, X},
title = {Chronosequencing methanogenic archaea in ancient Longji rice Terraces in China.},
journal = {Science bulletin},
volume = {62},
number = {12},
pages = {879-887},
doi = {10.1016/j.scib.2017.05.024},
pmid = {36659324},
issn = {2095-9281},
abstract = {Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty (CE 1361-1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial- and decadal-scale influences of known historical events, including social turbulences (The Taiping Rebellion, CE 1850-1865), palaeoclimate changes (the Little Ice Age) and recorded natural disasters (earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.},
}

@article {pmid36658397,
year = {2023},
author = {Laso-Pérez, R and Wu, F and Crémière, A and Speth, DR and Magyar, JS and Zhao, K and Krupovic, M and Orphan, VJ},
title = {Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {36658397},
issn = {2058-5276},
abstract = {'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.},
}

@article {pmid36639538,
year = {2023},
author = {Zhang, CJ and Liu, YR and Cha, G and Liu, Y and Zhou, XQ and Lu, Z and Pan, J and Cai, M and Li, M},
title = {Potential for mercury methylation by Asgard archaea in mangrove sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36639538},
issn = {1751-7370},
abstract = {Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The conversion of MeHg from mercury (Hg) is mediated by a variety of anaerobic microorganisms carrying hgcAB genes. Mangrove sediments are potential hotspots of microbial Hg methylation; however, the microorganisms responsible for Hg methylation are poorly understood. Here, we conducted metagenomic and metatranscriptomic analyses to investigate the diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems. The highest hgcA abundance and expression occurred in surface sediments in Shenzhen, where the highest MeHg concentration was also observed. We reconstructed 157 metagenome-assembled genomes (MAGs) carrying hgcA and identified several putative novel Hg-methylators, including one Asgard archaea (Lokiarchaeota). Further analysis of MAGs revealed that Deltaproteobacteria, Euryarchaeota, Bacteroidetes, Chloroflexi, and Lokiarchaeota were the most abundant and active Hg-methylating groups, implying their crucial role in MeHg production. By screening publicly available MAGs, 104 additional Asgard MAGs carrying hgcA genes were identified from a wide range of coast, marine, permafrost, and lake sediments. Protein homology modelling predicts that Lokiarchaeota HgcAB proteins contained the highly conserved amino acid sequences and folding structures required for Hg methylation. Phylogenetic tree revealed that hgcA genes from Asgard clustered with fused hgcAB genes, indicating a transitional stage of Asgard hgcA genes. Our findings thus suggest that Asgard archaea are potential novel Hg-methylating microorganisms and play an important role in hgcA evolution.},
}

@article {pmid36622233,
year = {2023},
author = {Jia, Y and Lahm, M and Chen, Q and Powers, L and Gonsior, M and Chen, F},
title = {The Predominance of Ammonia-Oxidizing Archaea in an Oceanic Microbial Community Amended with Cyanobacterial Lysate.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0240522},
doi = {10.1128/spectrum.02405-22},
pmid = {36622233},
issn = {2165-0497},
abstract = {When the oligotrophic microbial community was amended with Synechococcus-derived dissolved organic matter (SDOM) and incubated under the dark condition, archaea relative abundance was initially very low but made up more than 60% of the prokaryotic community on day 60, and remained dominant for at least 9 months. The archaeal sequences were dominated by Candidatus Nitrosopumilus, the Group I.1a Thaumarchaeota. The increase of Thaumarchaeota in the dark incubation corresponded to the period of delayed ammonium oxidation upon an initially steady increase in ammonia, supporting the remarkable competency of Thaumarchaeota in energy utilization and fixation of inorganic carbon in the ocean. IMPORTANCE Thaumarchaeota, which are ammonia-oxidizing archaea (AOA), are mainly chemolithoautotrophs that can fix inorganic carbon to produce organic matter in the dark. Their distinctive physiological traits and high abundance in the water column indicate the significant ecological roles they play in the open ocean. In our study, we found predominant Thaumarchaeota in the microbial community amended with cyanobacteria-derived lysate under the dark condition. Furthermore, Thaumarchaeota remained dominant in the microbial community even after 1 year of incubation. Through the ammonification process, dissolved organic matter (DOM) from cyanobacterial lysate was converted to ammonium which was used as an energy source for Thaumarchaeota to fix inorganic carbon into biomass. Our study further advocates the important roles of Thaumarchaeota in the ocean's biogeochemical cycle.},
}

@article {pmid36584837,
year = {2022},
author = {Yang, WT and Shen, LD and Bai, YN},
title = {Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems.},
journal = {Environmental research},
volume = {219},
number = {},
pages = {115174},
doi = {10.1016/j.envres.2022.115174},
pmid = {36584837},
issn = {1096-0953},
abstract = {Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH4). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH4 emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH4 emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH4 sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH4 mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.},
}

@article {pmid36573238,
year = {2022},
author = {Moll, J and Hoppe, B},
title = {Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14567},
pmid = {36573238},
issn = {2167-8359},
abstract = {Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.},
}

@article {pmid36567186,
year = {2022},
author = {Zhang, X and Zhang, C and Liu, Y and Zhang, R and Li, M},
title = {Non-negligible roles of archaea in coastal carbon biogeochemical cycling.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2022.11.008},
pmid = {36567186},
issn = {1878-4380},
abstract = {Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO2 fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.},
}

@article {pmid36552364,
year = {2022},
author = {Li, Q and Wang, N and Han, W and Zhang, B and Zang, J and Qin, Y and Wang, L and Liu, J and Zhang, T},
title = {Soil Geochemical Properties Influencing the Diversity of Bacteria and Archaea in Soils of the Kitezh Lake Area, Antarctica.},
journal = {Biology},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/biology11121855},
pmid = {36552364},
issn = {2079-7737},
abstract = {It is believed that polar regions are influenced by global warming more significantly, and because polar regions are less affected by human activities, they have certain reference values for future predictions. This study aimed to investigate the effects of climate warming on soil microbial communities in lake areas, taking Kitezh Lake, Antarctica as the research area. Below-peak soil, intertidal soil, and sediment were taken at the sampling sites, and we hypothesized that the diversity and composition of the bacterial and archaeal communities were different among the three sampling sites. Through 16S rDNA sequencing and analysis, bacteria and archaea with high abundance were obtained. Based on canonical correspondence analysis and redundancy analysis, pH and phosphate had a great influence on the bacterial community whereas pH and nitrite had a great influence on the archaeal community. Weighted gene coexpression network analysis was used to find the hub bacteria and archaea related to geochemical factors. The results showed that in addition to pH, phosphate, and nitrite, moisture content, ammonium, nitrate, and total carbon content also play important roles in microbial diversity and structure at different sites by changing the abundance of some key microbiota.},
}

@article {pmid36544005,
year = {2022},
author = {Löwe, J},
title = {Mysterious Asgard archaea microbes reveal their inner secrets.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {36544005},
issn = {1476-4687},
}

@article {pmid36543797,
year = {2022},
author = {Zhao, W and Zhong, B and Zheng, L and Tan, P and Wang, Y and Leng, H and de Souza, N and Liu, Z and Hong, L and Xiao, X},
title = {Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {7861},
pmid = {36543797},
issn = {2041-1723},
abstract = {Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.},
}

@article {pmid36541769,
year = {2022},
author = {Bai, T and Pu, X and Guo, X and Liu, J and Zhao, L and Zhang, X and Zhang, S and Cheng, L},
title = {Effects of Dietary Nonfibrous Carbohydrate/Neutral Detergent Fiber Ratio on Methanogenic Archaea and Cellulose-Degrading Bacteria in the Rumen of Karakul Sheep: a 16S rRNA Gene Sequencing Study.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0129122},
doi = {10.1128/aem.01291-22},
pmid = {36541769},
issn = {1098-5336},
abstract = {The study was conducted to investigate the effects of dietary nonfibrous carbohydrate (NFC)/neutral detergent fiber (NDF) ratio on methanogenic archaea and cellulose-degrading bacteria in Karakul sheep by 16S rRNA gene sequencing. Twelve Karakul sheep were randomly divided into four groups, each group with three replicates, and they were fed with four dietary NFC/NDF ratios at 0.54, 0.96, 1.37, and 1.90 as groups 1, 2, 3, and 4, respectively. The experiment lasted for four periods: I (1 to 18 days), II (19 to 36 days), III (37 to 54 days), and IV (55 to 72 days); during each period, rumen contents were collected before morning feeding to investigate on methanogenic archaea and cellulose-degrading bacteria. The results showed that with an increase in dietary NFC/NDF ratio, the number of rumen archaea operational taxonomic units and the diversity of archaea decrease. The most dominant methanogens did not change with dietary NFC/NDF ratio and prolongation of experimental periods. Methanobrevibacter was the most dominant genus. At the species level, the relative abundance of Methanobrevibacter ruminantium first increased and then decreased when the NFC/NDF ratio increased. When the dietary NFC/NDF ratio was 0.96, the structure of archaea was largely changed, and the relative abundance of Fibrobacter sp. strain UWCM, Ruminococcus flavefaciens, and Ruminococcus albus were the highest. When the dietary NFC/NDF ratio was 1.37, the relative abundance of Butyrivibrio fibrisolvens was higher than for other groups. Based on all the data, we concluded that a dietary NFC/NDF ratio of ca. 0.96 to 1.37 was a suitable ratio to support optimal sheep production. IMPORTANCE CH4 produced by ruminants aggravates the greenhouse effect and cause wastage of feed energy, and CH4 emissions are related to methanogens. According to the current literature, there is a symbiotic relationship between methanogens and cellulolytic bacteria, so reducing methane will inevitably affect the degradation of fiber materials. This experiment used 16S rRNA gene high-throughput sequencing technology to explore the balance relationship between methanogens and cellulolytic bacteria for the first time through a long-term feeding period. The findings provide fundamental data, supporting for the diet structures with potential to reduce CH4 emission.},
}

@article {pmid36529166,
year = {2022},
author = {Jiang, Z and Tang, S and Liao, Y and Li, S and Wang, S and Zhu, X and Ji, G},
title = {Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {137585},
doi = {10.1016/j.chemosphere.2022.137585},
pmid = {36529166},
issn = {1879-1298},
abstract = {Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N2O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N2O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N2O through lab-scale subsurface CWs. The N2O emission flux of CW at 8 °C was 1.23 mg m[-2]·h[-1], significantly lower than that at 25 °C (1.92 mg m[-2]·h[-1]). The contribution of ammonia oxidation to N2O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N2O production from AOA increased from 1.91 ng N·g[-1] at 25 °C to 4.11 ng N·g[-1] soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N2O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N2O at low temperature.},
}

@article {pmid36519377,
year = {2022},
author = {Kucukyildirim, S and Ozdemirel, HO and Lynch, M},
title = {Similar mutation rates but different mutation spectra in moderate and extremely halophilic archaea.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkac303},
pmid = {36519377},
issn = {2160-1836},
abstract = {Archaea are a major part of Earth`s microbiota and extremely diverse. Yet, we know very little about the process of mutation that drives such diversification. To expand beyond previous work with the moderate halophilic archaeal species Haloferax volcanii, we performed a mutation-accumulation experiment followed by whole-genome sequencing in the extremely halophilic archaeon Halobacterium salinarum. Although H. volcanii and H. salinarum have different salt requirements, both species have highly polyploid genomes and similar GC content. We accumulated mutations for an average of 1250-generations in 67 mutation accumulation lines of H. salinarum, and revealed 84 single-base substitutions and 10 insertion-deletion mutations. The estimated base-substitution mutation rate of 3.99 × 10-10 per site per generation or 1.0 × 10-3 per genome per generation in H. salinarum is similar to that reported for H. volcanii (1.2 × 10-3 per genome per generation), but the genome-wide insertion-deletion rate and spectrum of mutations are somewhat dissimilar in these archaeal species. The spectra of spontaneous mutations were AT biased in both archaea, but they differed in significant ways that may be related to differences in the fidelity of DNA replication/repair mechanisms or a simple result of the different salt concentrations.},
}

@article {pmid36512566,
year = {2022},
author = {, },
title = {Expression of Concern: A Versatile Medium for Cultivating Methanogenic Archaea.},
journal = {PloS one},
volume = {17},
number = {12},
pages = {e0278740},
pmid = {36512566},
issn = {1932-6203},
}

@article {pmid36499474,
year = {2022},
author = {Ginsbach, LF and Gonzalez, JM},
title = {Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures.},
journal = {International journal of molecular sciences},
volume = {23},
number = {23},
pages = {},
pmid = {36499474},
issn = {1422-0067},
mesh = {*Archaea/metabolism ; Phylogeny ; *Methane/metabolism ; Temperature ; Hot Temperature ; },
abstract = {Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.},
}

*Archaea/metabolism
Phylogeny
*Methane/metabolism
Temperature
Hot Temperature

@article {pmid36461738,
year = {2022},
author = {Ponlachantra, K and Suginta, W and Robinson, RC and Kitaoku, Y},
title = {AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2200119},
doi = {10.1002/bies.202200119},
pmid = {36461738},
issn = {1521-1878},
abstract = {The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.},
}

@article {pmid36445127,
year = {2022},
author = {Woo, Y and Cruz, MC and Wuertz, S},
title = {Selective Enrichment of Nitrososphaera viennensis-Like Ammonia-Oxidizing Archaea over Ammonia-Oxidizing Bacteria from Drinking Water Biofilms.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0184522},
doi = {10.1128/spectrum.01845-22},
pmid = {36445127},
issn = {2165-0497},
abstract = {Ammonia-oxidizing archaea (AOA) can oxidize ammonia to nitrite for energy gain. They have been detected in chloraminated drinking water distribution systems (DWDS) along with the more common ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, no members of the AOA have been isolated or enriched from drinking water environments. To begin the investigation of the role of AOA in chloraminated DWDS, we developed a selective approach using biofilm samples from a full-scale operational network as inoculum. A Nitrososphaera viennensis-like AOA taxon was enriched from a mixed community that also included Nitrosomonas-like AOB while gradually scaling up the culture volume. Dimethylthiourea (DMTU) and pyruvate at 100 μM were added to promote the growth of AOA while inhibiting AOB. This resulted in the eventual washout of AOB, while NOB were absent after 2 or 3 rounds of amendment with 24 μM sodium azide. The relative abundance of AOA in the enrichment increased from 0.2% to 39.5% after adding DMTU and pyruvate, and further to 51.6% after filtration through a 0.45-μm pore size membrane, within a period of approximately 6 months. IMPORTANCE Chloramination has been known to increase the risk of nitrification episodes in DWDS due to the presence of ammonia-oxidizing microorganisms. Among them, AOB are more frequently detected than AOA. All publicly available cultures of AOA have been isolated from soil, marine or surface water environments, meaning they are allochthonous to DWDS. Hence, monochloramine exposure studies involving these strains may not accurately reflect their role in DWDS. The described method allows for the rapid enrichment of autochthonous AOA from drinking water nitrifying communities. The high relative abundance of AOA in the resulting enrichment culture reduces any confounding effects of co-existing heterotrophic bacteria when investigating the response of AOA to varied levels of monochloramine in drinking water.},
}

@article {pmid36444822,
year = {2022},
author = {Hagagy, N and Abdel-Mawgoud, M and Akhtar, N and Selim, S and AbdElgawad, H},
title = {The new isolated Archaea strain improved grain yield, metabolism and quality of wheat plants under Co stress conditions.},
journal = {Journal of plant physiology},
volume = {280},
number = {},
pages = {153876},
doi = {10.1016/j.jplph.2022.153876},
pmid = {36444822},
issn = {1618-1328},
abstract = {Heavy metal (e.g. cobalt) pollution causes a serious of environmental and agricultural problems. On the other hand, plant growth-promoting microorganisms enhance plant growth and mitigate heavy metal stress. Herein, we isolated and identified the unclassified species strain NARS9, belong to Haloferax,. Cobalt (Co, 200 mg/kg soil) stress mitigating impact of the identified on wheat grains yield, primary and secondary metabolism and grain quality was investigated. Co alone significantly induced Co accumulation in wheat grain (260%), and consequently reduced wheat yield (130%) and quality. Haloferax NARS9 alone significantly enhanced grain chemicals composition (i.e., total sugars (89%) and organic acids (e.g., oxalic and isobutyric acids), essential amino acids (e.g., threonine, lysine, and histidine) and unsaturated fatty acids (e.g. eicosenoic, erucic and tetracosenoic acids). Interestingly, Co stress induced wheat grain yield, reduction were significantly mitigated by Haloferax NARS9 treatment by 26% compared to Co stress alone. Under Co stress, Haloferax NARS9 significantly increased sugar metabolism including sucrose and starch levels and their metabolic enzymes (i.e. invertases, sucrose synthase, starch synthase). This in turn increased organic acid (e.g. oxalic (70%) and malic acids (60%)) and amino acids. levels and biosynthetic enzymes, e.g. glutamine synthetase and threonine synthase. Increased sugars levels by Haloferax NARS9 under Co treatment also provided a route for the biosynthesis of saturated fatty acids, particularly palmitic and stearic acids. Furthermore, Haloferax NARS9 treatment supported the wheat nutritive value through increasing minerals (Ca, Fe, Mn, Zn) and antioxidants i.e., polyphenol, flavonoids, ASC and GSH and total polyamines by 50%, 110%, 400%, 30%, and 90% respectively). These in parallel with the increase in the activity of (phenylalanine ammonia-lyase (110%) in phenolic metabolism). Overall, this study demonstrates the potentiality of Haloferax NARS9 in harnessing carbon and nitrogen metabolism differentially in wheat plants to cope with Co toxicity. Our results also suggested that the use of Haloferax NARS9 in agricultural fields can improve growth and nutritional value of wheat grains.},
}

@article {pmid36434094,
year = {2022},
author = {Sato, T and Utashima, SH and Yoshii, Y and Hirata, K and Kanda, S and Onoda, Y and Jin, JQ and Xiao, S and Minami, R and Fukushima, H and Noguchi, A and Manabe, Y and Fukase, K and Atomi, H},
title = {A non-carboxylating pentose bisphosphate pathway in halophilic archaea.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1290},
pmid = {36434094},
issn = {2399-3642},
mesh = {*Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; *Ribose/metabolism ; Pentoses/metabolism ; Archaea/genetics/metabolism ; Guanosine/metabolism ; Phosphates ; },
abstract = {Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.},
}

*Ribulose-Bisphosphate Carboxylase/genetics/metabolism
*Ribose/metabolism
Pentoses/metabolism
Archaea/genetics/metabolism
Guanosine/metabolism
Phosphates

@article {pmid36414709,
year = {2022},
author = {Lee, S and Sieradzki, ET and Nicol, GW and Hazard, C},
title = {Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36414709},
issn = {1751-7370},
abstract = {Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived [13]C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of [13]C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of [13]C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in [13]C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.},
}

@article {pmid36413802,
year = {2022},
author = {Matse, DT and Jeyakumar, P and Bishop, P and Anderson, CWN},
title = {Copper induces nitrification by ammonia-oxidizing bacteria and archaea in pastoral soils.},
journal = {Journal of environmental quality},
volume = {},
number = {},
pages = {},
doi = {10.1002/jeq2.20440},
pmid = {36413802},
issn = {1537-2537},
abstract = {Copper (Cu) is the main co-factor in the functioning of the ammonia monooxygenase (AMO) enzyme, which is responsible for the first step of ammonia oxidation. We report a greenhouse-based pot experiment that examines the response of ammonia-oxidizing bacteria and archaea (AOB and AOA) to different bioavailable Cu concentrations in three pastoral soils (Recent, Pallic, and Pumice soils) planted with ryegrass (Lolium perenne L.). Five treatments were used: control (no urine and Cu), urine only at 300 mg N kg[-1] soil (Cu0), urine + 1 mg Cu kg[-1] soil (Cu1), urine + 10 mg Cu kg[-1] soil (Cu10), and urine + 100 mg Cu kg[-1] soil (Cu100). Pots were destructively sampled at Day 0, 1, 7, 15, and 25 after urine application. The AOB/AOA amoA gene abundance was analyzed by real-time quantitative polymerase chain reaction at Days 1 and 15. The AOB amoA gene abundance increased 10.0- and 22.6-fold in the Recent soil and 2.1- and 2.5-fold in the Pallic soil for the Cu10 compared with Cu0 on Days 1 and 15, respectively. In contrast, the Cu100 was associated with a reduction in AOB amoA gene abundance in the Recent and Pallic soils but not in the Pumice soil. This may be due to the influence of soil cation exchange capacity differences on the bioavailable Cu. Bioavailable Cu in the Recent and Pallic soils influenced nitrification and AOB amoA gene abundance, as evidenced by the strong positive correlation between bioavailable Cu, nitrification, and AOB amoA. However, bioavailable Cu did not influence the nitrification and AOA amoA gene abundance increase.},
}

@article {pmid36406397,
year = {2022},
author = {Yuan, H and Zhang, W and Yin, H and Zhang, R and Wang, J},
title = {Taxonomic dependency of beta diversity for bacteria, archaea, and fungi in a semi-arid lake.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {998496},
pmid = {36406397},
issn = {1664-302X},
abstract = {Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of Proteobacteria, Chloroflexi, Euryarchaeota, and Rozellomycota increased toward deep water, while Acidobacteria, Parvarchaeota, and Chytridiomycota decreased. For bacteria and archaea, there were significant (p < 0.05) decreasing water-depth patterns for LCBD and LCBDRepl (i.e., species replacement), while increasing patterns for total beta diversity and turnover, implying that total beta diversity and LCBD were dominated by species turnover or LCBDRepl. Further, bacteria showed a strong correlation with archaea regarding LCBD, total beta diversity and turnover. Such parallel patterns among bacteria and archaea were underpinned by similar ecological processes like environmental selection. Total beta diversity and turnover were largely affected by sediment total nitrogen, while LCBD and LCBDRepl were mainly constrained by water NO2 [-]-N and NO3 [-]-N. For fungal community variation, no significant patterns were observed, which may be due to different drivers like water nitrogen or phosphorus. Taken together, our findings provide compelling evidences for disentangling the underlying mechanisms of community variation in multiple aquatic microbial taxonomic groups.},
}

@article {pmid36402873,
year = {2022},
author = {Hu, L and Dong, Z and Wang, Z and Xiao, L and Zhu, B},
title = {The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N2O emission in alkaline and neutral purple soils.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19928},
pmid = {36402873},
issn = {2045-2322},
mesh = {*Archaea/genetics ; Nitrification ; Soil/chemistry ; Ammonia ; Soil Microbiology ; Bacteria/genetics ; Oxidation-Reduction ; *Betaproteobacteria/genetics ; },
abstract = {Nitrification is believed to be one of the primary processes of N2O emission in the agroecological system, which is controlled by soil microbes and mainly regulated by soil pH, oxygen content and NH4[+] availability. Previous studies have proved that the relative contributions of ammonia oxidizing bacteria (AOB) and archaea (AOA) to N2O production were varied with soil pH, however, there is still no consensus on the regulating mechanism of nitrification-derived N2O production by soil pH. In this study, 1-octyne (a selective inhibitor of AOB) and acetylene (an inhibitor of AOB and AOA) were used in a microcosm incubation experiment to differentiate the relative contribution of AOA and AOB to N2O emissions in a neutral (pH = 6.75) and an alkaline (pH = 8.35) soils. We found that the amendment of ammonium (NH4[+]) observably stimulated the production of both AOA and AOB-related N2O and increased the ammonia monooxygenase (AMO) gene abundances of AOA and AOB in the two test soils. Among which, AOB dominated the process of ammonia oxidation in the alkaline soil, contributing 70.8% of N2O production derived from nitrification. By contrast, the contribution of AOA and AOB accounted for about one-third of nitrification-related N2O in acidic soil, respectively. The results indicated that pH was a key factor to change abundance and activity of AOA and AOB, which led to the differentiation of derivation of N2O production in purple soils. We speculate that both NH4[+] content and soil pH mediated specialization of ammonia-oxidizing microorganisms together; and both specialization results and N2O yield led to the different N2O emission characteristics in purple soils. These results may help inform the development of N2O reduction strategies in the future.},
}

*Archaea/genetics
Nitrification
Soil/chemistry
Ammonia
Soil Microbiology
Bacteria/genetics
Oxidation-Reduction
*Betaproteobacteria/genetics

@article {pmid36400771,
year = {2022},
author = {Schoelmerich, MC and Ouboter, HT and Sachdeva, R and Penev, PI and Amano, Y and West-Roberts, J and Welte, CU and Banfield, JF},
title = {A widespread group of large plasmids in methanotrophic Methanoperedens archaea.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {7085},
pmid = {36400771},
issn = {2041-1723},
mesh = {*Archaea/metabolism ; Anaerobiosis ; *Methane/metabolism ; Oxidation-Reduction ; Plasmids/genetics ; },
abstract = {Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane, yet their extrachromosomal genetic elements are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments. By manual curation we show that two of the plasmids are large (155,605 bp and 191,912 bp), circular, and may replicate bidirectionally. The plasmids occur in the same copy number as the main chromosome, and plasmid genes are actively transcribed. One of the plasmids encodes three tRNAs, ribosomal protein uL16 and elongation factor eEF2; these genes appear to be missing in the host Methanoperedens genome, suggesting an obligate interdependence between plasmid and host. Our work opens the way for the development of genetic vectors to shed light on the physiology and biochemistry of Methanoperedens, and potentially genetically edit them to enhance growth and accelerate methane oxidation rates.},
}

*Archaea/metabolism
Anaerobiosis
*Methane/metabolism
Oxidation-Reduction
Plasmids/genetics

@article {pmid36385454,
year = {2022},
author = {Zhou, Y and Zhou, L and Yan, S and Chen, L and Krupovic, M and Wang, Y},
title = {Diverse viruses of marine archaea discovered using metagenomics.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16287},
pmid = {36385454},
issn = {1462-2920},
abstract = {During the past decade, metagenomics became a method of choice for the discovery of novel viruses. However, host assignment for uncultured viruses remains challenging, especially for archaeal viruses, which are grossly undersampled compared to viruses of bacteria and eukaryotes. Here, we assessed the utility of CRISPR spacer targeting, tRNA gene matching and homology searches for viral signature proteins, such as major capsid proteins, for the assignment of archaeal hosts and validated these approaches on metaviromes from Yangshan Harbor (YSH). We report 35 new genomes of viruses which could be confidently assigned to hosts representing diverse lineages of marine archaea. We show that the archaeal YSH virome is highly diverse, with some viruses enriching the previously described virus groups, such as magroviruses of Marine Group II Archaea (Poseidoniales), and others representing novel groups of marine archaeal viruses. Metagenomic recruitment of Tara Oceans datasets on the YSH viral genomes demonstrated the presence of YSH Poseidoniales and Nitrososphaeria viruses in the global oceans, but also revealed the endemic YSH-specific viral lineages. Furthermore, our results highlight the relationship between the soil and marine thaumarchaeal viruses. We propose three new families within the class Caudoviricetes for the classification of the five complete viral genomes predicted to replicate in marine Poseidoniales and Nitrososphaeria, two ecologically important and widespread archaeal groups. This study illustrates the utility of viral metagenomics in exploring the archaeal virome and provides new insights into the diversity, distribution and evolution of marine archaeal viruses.},
}

@article {pmid36383678,
year = {2022},
author = {Ghaly, TM and Tetu, SG and Penesyan, A and Qi, Q and Rajabal, V and Gillings, MR},
title = {Discovery of integrons in Archaea: Platforms for cross-domain gene transfer.},
journal = {Science advances},
volume = {8},
number = {46},
pages = {eabq6376},
pmid = {36383678},
issn = {2375-2548},
abstract = {Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.},
}

@article {pmid36372432,
year = {2022},
author = {Kuroda, K and Kubota, K and Kagemasa, S and Nakai, R and Hirakata, Y and Yamamoto, K and Nobu, MK and Narihiro, T},
title = {Novel Cross-domain Symbiosis between Candidatus Patescibacteria and Hydrogenotrophic Methanogenic Archaea Methanospirillum Discovered in a Methanogenic Ecosystem.},
journal = {Microbes and environments},
volume = {37},
number = {4},
pages = {},
doi = {10.1264/jsme2.ME22063},
pmid = {36372432},
issn = {1347-4405},
mesh = {*Archaea/genetics ; Methanospirillum/genetics ; Symbiosis ; Ecosystem ; In Situ Hybridization, Fluorescence ; Phylogeny ; *Euryarchaeota ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {To identify novel cross-domain symbiosis between Candidatus Patescibacteria and Archaea, we performed fluorescence in situ hybridization (FISH) on enrichment cultures derived from methanogenic bioreactor sludge with the newly designed 32-520-1066 probe targeting the family-level uncultured clade 32-520/UBA5633 lineage in the class Ca. Paceibacteria. All FISH-detectable 32-520/UBA5633 cells were attached to Methanospirillum, indicating high host specificity. Transmission electron microscopy observations revealed 32-520/UBA5633-like cells that were specifically adherent to the plug structure of Methanospirillum-like rod-shaped cells. The metagenome-assembled genomes of 32-520/UBA5633 encoded unique gene clusters comprising pilin signal peptides and type IV pilins. These results provide novel insights into unseen symbiosis between Ca. Patescibacteria and Archaea.},
}

*Archaea/genetics
Methanospirillum/genetics
Symbiosis
Ecosystem
In Situ Hybridization, Fluorescence
Phylogeny
*Euryarchaeota
Bacteria/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid36367391,
year = {2022},
author = {Boyd, ES and Spietz, RL and Kour, M and Colman, DR},
title = {A naturalist perspective of microbiology: Examples from methanogenic archaea.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16285},
pmid = {36367391},
issn = {1462-2920},
abstract = {Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.},
}

@article {pmid36358054,
year = {2022},
author = {Gu, S and Wang, R and Xing, H and Yu, M and Shen, S and Zhao, L and Sun, J and Li, Y},
title = {Effects of different low temperature conditions on anaerobic digestion efficiency of pig manure and composition of archaea community.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {86},
number = {5},
pages = {1181-1192},
doi = {10.2166/wst.2022.267},
pmid = {36358054},
issn = {0273-1223},
mesh = {Swine ; Animals ; *Manure ; *Archaea/metabolism ; Anaerobiosis ; Temperature ; Fatty Acids, Volatile/metabolism ; Bioreactors ; Methane/metabolism ; },
abstract = {To explore the effect of low temperature on the anaerobic digestion of pig manure, the anaerobic digestion experiment was carried out under the conditions of inoculum concentration of 30% and TS of 8%. Five low-temperature gradients of 4, 8, 12, 16 and 20 °C were set to study the activities of gas production, pH, solluted chemical oxygen demand (SCOD), volatile fatty acids (VFAs), coenzymes F420 and archaea community composition in the digestion process. The results were demonstrated: as the temperature decreased, the more unstable the gas production became, the less gas production produced, and the later the gas peak occurred. There were no significant peaks at either 4 °C or 8 °C, and the SCOD was unstable over time. From 12 °C, the SCOD increased over time, and the higher the temperature, the faster the growth trend. The pH was always greater than 7.6. 8, 12, 16, 20 °C had different degrees of VFAs accumulation at the late digestion stage. The higher the temperature, the greater the amount of volatile acid accumulation. When the VFAs of each reactor reached the maximum, the proportion of acetic acid also reached the highest. The digestion system of the five treatment groups was dominated by hydrogen-nutrient methanogenic pathway. The results could provide a further reference for the mechanism of anaerobic digestion of pig manure at low temperatures.},
}

Swine
Animals
*Manure
*Archaea/metabolism
Anaerobiosis
Temperature
Fatty Acids, Volatile/metabolism
Bioreactors
Methane/metabolism

@article {pmid36350548,
year = {2023},
author = {Hepowit, NL and Maupin-Furlow, JA},
title = {Application of Archaea in Deubiquitinase-Like Enzyme Discovery and Activity Assay.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2591},
number = {},
pages = {151-169},
pmid = {36350548},
issn = {1940-6029},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {*Ubiquitins/metabolism ; *Archaea/metabolism ; Ubiquitin/metabolism ; Eukaryotic Cells/metabolism ; Deubiquitinating Enzymes ; },
abstract = {Archaea can be used as microbial platforms to discover new types of deubiquitinase-like (DUB-like) enzymes and to produce ubiquitin/ubiquitin-like (Ub/Ubl) protein conjugates as substrates for DUB/DUB-like activity assays. Here we outline how to use archaea to synthesize, purify, and assay the activity of DUB-like enzymes with unusual properties, including catalytic activity in hypersaline conditions, organic solvents, and high temperatures. We also outline the application of archaea in forming Ub/Ubl isopeptide linkages that include the covalent attachments of diverse archaeal and eukaryotic Ub/Ubls to target proteins. Archaea form these Ub/Ubl-linked protein conjugates in vivo, and the resulting products are found to serve as useful DUB substrates for in vitro assays.},
}

*Ubiquitins/metabolism
*Archaea/metabolism
Ubiquitin/metabolism
Eukaryotic Cells/metabolism
Deubiquitinating Enzymes

@article {pmid36332026,
year = {2022},
author = {Adam, PS and Kolyfetis, GE and Bornemann, TLV and Vorgias, CE and Probst, AJ},
title = {Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling.},
journal = {Science advances},
volume = {8},
number = {44},
pages = {eabm9651},
pmid = {36332026},
issn = {2375-2548},
abstract = {Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO2-reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called "methanogenesis markers" but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.},
}

@article {pmid36332013,
year = {2022},
author = {Verma, A and Åberg-Zingmark, E and Sparrman, T and Mushtaq, AU and Rogne, P and Grundström, C and Berntsson, R and Sauer, UH and Backman, L and Nam, K and Sauer-Eriksson, E and Wolf-Watz, M},
title = {Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.},
journal = {Science advances},
volume = {8},
number = {44},
pages = {eabm4089},
pmid = {36332013},
issn = {2375-2548},
mesh = {Humans ; *Archaea/genetics ; *Adenylate Kinase/chemistry ; Catalysis ; Catalytic Domain ; },
abstract = {Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while [19]F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.},
}

Humans
*Archaea/genetics
*Adenylate Kinase/chemistry
Catalysis
Catalytic Domain

@article {pmid36316034,
year = {2023},
author = {Peiter, N and Rother, M},
title = {In vivo probing of SECIS-dependent selenocysteine translation in Archaea.},
journal = {Life science alliance},
volume = {6},
number = {1},
pages = {},
pmid = {36316034},
issn = {2575-1077},
mesh = {*Selenocysteine/genetics ; Archaea/genetics ; *Selenium ; 3' Untranslated Regions ; Base Sequence ; Selenoproteins/genetics ; },
abstract = {Cotranslational insertion of selenocysteine (Sec) proceeds by recoding UGA to a sense codon. This recoding is governed by the Sec insertion sequence (SECIS) element, an RNA structure on the mRNA, but size, location, structure determinants, and mechanism differ for Bacteria, Eukarya, and Archaea. For Archaea, the structure-function relation of the SECIS is poorly understood, as only rather laborious experimental approaches are established. Furthermore, these methods do not allow for quantitative probing of Sec insertion. In order to overcome these limitations, we engineered bacterial β-lactamase into an archaeal selenoprotein, thereby establishing a reporter system, which correlates enzyme activity to Sec insertion. Using this system, in vivo Sec insertion depending on the availability of selenium and the presence of a SECIS element was assessed in Methanococcus maripaludis Furthermore, a minimal SECIS element required for Sec insertion in M. maripaludis was defined and a conserved structural motif shown to be essential for function. Besides developing a convenient tool for selenium research, converting a bacterial enzyme into an archaeal selenoprotein provides proof of concept that novel selenoproteins can be engineered in Archaea.},
}

*Selenocysteine/genetics
Archaea/genetics
*Selenium
3' Untranslated Regions
Base Sequence
Selenoproteins/genetics

@article {pmid36314867,
year = {2022},
author = {Cha, G and Liu, Y and Yang, Q and Bai, L and Cheng, L and Fan, W},
title = {Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {22},
pages = {e0157422},
pmid = {36314867},
issn = {1098-5336},
mesh = {*Archaea ; Phylogeny ; Ligands ; *Genomics ; Ecosystem ; },
abstract = {Diverse archaea, including many unknown species and phylogenetically deeply rooted taxa, survive in extreme environments. They play crucial roles in the global carbon cycle and element fluxes in many terrestrial, marine, saline, host-associated, hot-spring, and oilfield environments. There is little knowledge of the diversity of chemoreceptors that are presumably involved in their habitat adaptation. Thus, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. The results show that chemoreceptors are significantly richer in archaea of mild environments than in those of extreme environments, that specific ligand-binding domains of the chemoreceptors are strongly associated with specific habitats, and that the number of chemoreceptors correlates with genome size. The results indicate that the successful adaptation of archaea to specific habitats has been associated with the acquisition and maintenance of chemoreceptors, which may be crucial for their survival in these environments. IMPORTANCE Archaea are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but general principles regarding how an archaeal species organizes its chemoreceptor diversity and habitat adaptation are poorly understood. Here, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. Signaling sensing and adaptation processes are tightly related to the ligand-binding domain, and it is clear that evolution and natural selection in specialized niches under constant conditions have selected for smaller genome sizes. Taken together, our results extend the understanding of archaeal adaptations to different environments and emphasize the importance of ecological constraints in shaping their evolution.},
}

*Archaea
Phylogeny
Ligands
*Genomics
Ecosystem

@article {pmid36301308,
year = {2022},
author = {Khan, F and Kaza, S},
title = {Crystal structure of an L-type lectin domain from archaea.},
journal = {Proteins},
volume = {},
number = {},
pages = {},
doi = {10.1002/prot.26440},
pmid = {36301308},
issn = {1097-0134},
abstract = {The crystal structures of an L-type lectin domain from Methanocaldococcus jannaschii in apo and mannose-bound forms have been determined. A thorough investigation of L-type lectin domains from several organisms provides insight into the differences in these domains from different kingdoms of life. While the overall fold of the L-type lectin domain is conserved, differences in the lengths of the carbohydrate-binding loops and significant variations in the Mn[2+] -binding site compared to the Ca[2+] -binding site are observed. Furthermore, the sequence and phylogenetic analyses suggest that the archaeal L-type lectin domain is evolutionarily closer to the plant legume lectins than to its bacterial or animal counterparts. This is the first report of the biochemical, structural, sequence, and phylogenetic analyses of an L-type lectin domain from archaea and serves to enhance our understanding of the species-specific differences and evolution of L-type lectin domains.},
}

@article {pmid36280648,
year = {2022},
author = {Baati, H and Siala, M and Azri, C and Ammar, E and Trigui, M},
title = {Hydrolytic enzyme screening and carotenoid production evaluation of halophilic archaea isolated from highly heavy metal-enriched solar saltern sediments.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {53},
number = {4},
pages = {1893-1906},
pmid = {36280648},
issn = {1678-4405},
mesh = {RNA, Ribosomal, 16S/genetics ; *Carotenoids ; Antioxidants ; Archaea/genetics ; *Metals, Heavy ; },
abstract = {This paper aimed to screen the enzymatic activities and evaluate the carotenoid production level of twenty-two halophilic archaea isolated from Sfax solar saltern sediments. The molecular identification performed by sequencing the 16S rRNA genes showed that all strains have a high similarity degree (99.7-100%) with Halobacterium salinarum NRC-1. The strains were screened for the presence of eight hydrolase activities using agar plate-based assays. The most detected enzyme was gelatinase (77.27% of total strains), followed by protease (63.63%) and amylase activities (50%). The carotenoid production yields of the strains ranged between 2.027 and 14.880 mg/l. The UV-Visible spectroscopy of pigments revealed that it was a bacterioruberin type. When evaluated and compared to the standard β-carotene, the antioxidant capacities of these pigments showed a scavenging activity of more than 75% at a concentration of 5 μg/ml for three strains (AS16, AS17, and AS18). Then a sequence of one-step optimization processes was performed, using the one-factor-at-a-time approach, to define the optimum conditions for growth and carotenoid production of the highest carotenoid producing strain (AS17). Different environmental factors and nutritional conditions were tested. Variations in these factors were found to deeply influence growth and carotenoid production. A maximum carotenoid production (16.490 mg/l), higher than that of the control (14.880 mg/l), was observed at 37 °C, pH 7, 250 g/l of salinity, with 80% air phase in the flask at 110 rpm, in presence of light and in culture media containing (g/l) 10, yeast extract; 7.5, casamino acid; 20, MgSO4; 4, KCl; and 3, trisodium citrate.},
}

RNA, Ribosomal, 16S/genetics
*Carotenoids
Antioxidants
Archaea/genetics
*Metals, Heavy

@article {pmid36270146,
year = {2022},
author = {Yan, G and Sun, X and Dong, Y and Gao, W and Gao, P and Li, B and Yan, W and Zhang, H and Soleimani, M and Yan, B and Häggblom, MM and Sun, W},
title = {Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning.},
journal = {Water research},
volume = {226},
number = {},
pages = {119247},
doi = {10.1016/j.watres.2022.119247},
pmid = {36270146},
issn = {1879-2448},
mesh = {Humans ; *Archaea/genetics/metabolism ; *Metagenome ; Vanadates/metabolism ; Vanadium/metabolism ; Ecosystem ; Anaerobiosis ; Bacteria/genetics/metabolism ; Methane/metabolism ; Methanosarcina/genetics ; Oxidation-Reduction ; Isotopes ; DNA/metabolism ; },
abstract = {Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F420H2 dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.},
}

Humans
*Archaea/genetics/metabolism
*Metagenome
Vanadates/metabolism
Vanadium/metabolism
Ecosystem
Anaerobiosis
Bacteria/genetics/metabolism
Methane/metabolism
Methanosarcina/genetics
Oxidation-Reduction
Isotopes
DNA/metabolism

@article {pmid36266535,
year = {2022},
author = {Shao, N and Fan, Y and Chou, CW and Yavari, S and Williams, RV and Amster, IJ and Brown, SM and Drake, IJ and Duin, EC and Whitman, WB and Liu, Y},
title = {Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1113},
pmid = {36266535},
issn = {2399-3642},
mesh = {*Archaea/genetics/metabolism ; *Mesna/metabolism ; Oxidoreductases/metabolism ; Methane/metabolism ; },
abstract = {Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.},
}

*Archaea/genetics/metabolism
*Mesna/metabolism
Oxidoreductases/metabolism
Methane/metabolism

@article {pmid36266339,
year = {2022},
author = {Hocher, A and Borrel, G and Fadhlaoui, K and Brugère, JF and Gribaldo, S and Warnecke, T},
title = {Growth temperature and chromatinization in archaea.},
journal = {Nature microbiology},
volume = {7},
number = {11},
pages = {1932-1942},
pmid = {36266339},
issn = {2058-5276},
support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; MC-A658-5TY40/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Archaea/genetics ; Temperature ; *Proteomics ; Chromatin/genetics ; },
abstract = {DNA in cells is associated with proteins that constrain its structure and affect DNA-templated processes including transcription and replication. HU and histones are the main constituents of chromatin in bacteria and eukaryotes, respectively, with few exceptions. Archaea, in contrast, have diverse repertoires of nucleoid-associated proteins (NAPs). To analyse the evolutionary and ecological drivers of this diversity, we combined a phylogenomic survey of known and predicted NAPs with quantitative proteomic data. We identify the Diaforarchaea as a hotbed of NAP gain and loss, and experimentally validate candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis. Proteomic analysis across a diverse sample of 19 archaea revealed that NAP investment varies from <0.03% to >5% of total protein. This variation is predicted by growth temperature. We propose that high levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures, with implications for the origin of chromatin in both archaea and eukaryotes.},
}

*Archaea/genetics
Temperature
*Proteomics
Chromatin/genetics

@article {pmid36256551,
year = {2022},
author = {Xin, YJ and Bao, CX and Tan, S and Hou, J and Cui, HL},
title = {Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov., two extremely halophilic archaea isolated from Gobi saline soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.005543},
pmid = {36256551},
issn = {1466-5034},
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Soil ; DNA, Archaeal/genetics ; Base Composition ; Sequence Analysis, DNA ; Fatty Acids/chemistry ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; *Halobacteriaceae ; Glycolipids/chemistry ; Sulfates ; Phosphatidylglycerols/analysis ; Nucleotides ; Amino Acids ; Phosphatidic Acids/analysis ; Esters ; },
abstract = {Two extremely halophilic archaeal strains, PSR5[T] and PSR8[T], were isolated from a saline soil sample collected from the Tarim Basin, Xinjiang, PR China. Both strains had two copies of the 16S rRNA genes rrn1 and rrn2, showing 2.6 and 3.9% divergence, respectively. The rrn1 gene of PSR5[T] showed 98.4 and 95.3% similarity to the rrn1 and rrn2 genes of strain PSR8[T]; the rrn2 gene of PSR5[T] displayed 97.4 and 96.7% similarity to those of strain PSR8[T], respectively. Phylogenetic analyses based on the 16S rRNA and rpoB' genes revealed that strains PSR5[T] and PSR8[T] formed a single cluster, and then tightly clustered with the current four Haladaptatus species (93.5-97.1% similarities for the 16S rRNA gene and 89.3-90.9% similarities for the rpoB' gene, respectively). Several phenotypic characteristics differentiate strains PSR5[T] and PSR8[T] from current Haladaptatus members. The polar lipids of the two strains are phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester phosphatidylglycerol sulphate and three glycolipids. One of the glycolipids is sulphated mannosyl glucosyl diether, and the remaining two glycolipids are unidentified. The average nucleotide identity, in silico DNA-DNA hybridization, amino acid identity and percentage of conserved proteins values between the two strains were 88.5, 39.1, 89.3 and 72.8 %, respectively, much lower than the threshold values proposed as a species boundary. These values among the two strains and Haladaptatus members were 77.9-79.2, 22.0-23.5, 75.1-78.2 and 56.8-69.9 %, respectively, much lower than the recommended threshold values for species delimitation. These results suggested that strains PSR5[T] and PSR8[T] represent two novel species of Haladaptatus. Based on phenotypic, chemotaxonomic, genomic and phylogenetic properties, strains PSR5[T] (=CGMCC 1.16851[T]=JCM 34141[T]) and PSR8[T] (=CGMCC 1.17025[T]=JCM 34142[T]) represent two novel species of the genus Haladaptatus, for which the names Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov. are proposed.},
}

RNA, Ribosomal, 16S/genetics
Phylogeny
*Soil
DNA, Archaeal/genetics
Base Composition
Sequence Analysis, DNA
Fatty Acids/chemistry
DNA, Bacterial/genetics
Bacterial Typing Techniques
*Halobacteriaceae
Glycolipids/chemistry
Sulfates
Phosphatidylglycerols/analysis
Nucleotides
Amino Acids
Phosphatidic Acids/analysis
Esters

@article {pmid36253512,
year = {2022},
author = {van Wolferen, M and Pulschen, AA and Baum, B and Gribaldo, S and Albers, SV},
title = {The cell biology of archaea.},
journal = {Nature microbiology},
volume = {7},
number = {11},
pages = {1744-1755},
pmid = {36253512},
issn = {2058-5276},
support = {203276//Wellcome Trust/United Kingdom ; MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Archaea ; Phylogeny ; *Biological Evolution ; Eukaryota ; Ecology ; },
abstract = {The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.},
}

Humans
*Archaea
Phylogeny
*Biological Evolution
Eukaryota
Ecology

@article {pmid36251741,
year = {2022},
author = {Hofmann, M and Norris, PR and Malik, L and Schippers, A and Schmidt, G and Wolf, J and Neumann-Schaal, M and Hedrich, S},
title = {Metallosphaera javensis sp. nov., a novel species of thermoacidophilic archaea, isolated from a volcanic area.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.005536},
pmid = {36251741},
issn = {1466-5034},
mesh = {*Archaea/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Iron ; Nucleotides ; Phylogeny ; Quinones ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sugars ; Sulfides ; *Sulfolobaceae ; Sulfur ; Sulfur Compounds ; },
abstract = {A novel thermoacidophilic archeaon, strain J1[T] (=DSM 112778[T],=JCM 34702[T]), was isolated from a hot pool in a volcanic area of Java, Indonesia. Cells of the strain were irregular, motile cocci of 1.0-1.2 µm diameter. Aerobic, organoheterotrophic growth with casamino acids was observed at an optimum temperature of 70 °C in a range of 55-78 °C and at an optimum pH of 3 in a range of 1.5 to 5. Various organic compounds were utilized, including a greater variety of sugars than has been reported for growth of other species of the genus. Chemolithoautotrophic growth was observed with reduced sulphur compounds, including mineral sulphides. Ferric iron was reduced during anaerobic growth with elemental sulphur. Cellular lipids were calditoglycerocaldarchaeol and caldarchaeol with some derivates. The organism contained the respiratory quinone caldariellaquinone. On the basis of phylogenetic and chemotaxonomic comparison with its closest relatives, it was concluded that strain J1[T] represents a novel species, for which the name Metallosphaera javensis is proposed. Low DNA-DNA relatedness values (16S rRNA gene <98.4%, average nucleotide identity (ANI) <80.1%) distinguished J1[T] from other species of the genus Metallosphaera and the DNA G+C content of 47.3% is the highest among the known species of the genus.},
}

*Archaea/genetics
Bacterial Typing Techniques
Base Composition
DNA, Bacterial/genetics
Fatty Acids/chemistry
Iron
Nucleotides
Phylogeny
Quinones
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Sugars
Sulfides
*Sulfolobaceae
Sulfur
Sulfur Compounds

@article {pmid36239851,
year = {2022},
author = {Zheng, XW and Wu, ZP and Sun, YP and Wang, BB and Hou, J and Cui, HL},
title = {Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., Halorussus salinisoli sp. nov.: six extremely halophilic archaea isolated from solar saltern, salt lake and saline soil.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {3},
pages = {32},
pmid = {36239851},
issn = {1433-4909},
mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Esters ; Glycolipids ; *Halobacteriaceae ; *Lakes ; Nucleotides ; Phosphatidylglycerols ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; Sulfates ; },
abstract = {Six novel halophilic archaeal strains of XZYJT10[T], XZYJ18[T], XZYJT40[T], XZYJT49[T], YCN54[T] and LT46[T] were isolated from a solar saltern in Tibet, a salt lake in Shanxi, and a saline soil in Xinjiang, China. Sequence similarities of 16S rRNA and rpoB' genes among strains XZYJT10[T], XZYJ18[T], XZYJT40[T], XZYJT49[T], YCN54[T], LT46[T] and current members of Halorussus were 90.6-97.8% and 87.8-96.4%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among these six strains and current Halorussus members were in the range of 76.5-87.5% and 21.0-33.8%, respectively. These values were all below the species boundary threshold values. The phylogenomic tree based on 122 conserved archaeal protein marker genes revealed that the six novel strains formed individual distinct branches and clustered tightly with Halorussus members. Several phenotypic characteristics distinguished the six strains from current Halorussus members. Polar lipid analysis showed that the six novel strains contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and two to three glycolipids. Phenotypic, chemotaxonomic and phylogenetic properties showed that the six strains represented six novel species within the genus Halorussus, for which the names Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., and Halorussus salinisoli sp. nov. are proposed.},
}

Base Composition
China
DNA, Archaeal/genetics
Esters
Glycolipids
*Halobacteriaceae
*Lakes
Nucleotides
Phosphatidylglycerols
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Soil
Sulfates

@article {pmid36232866,
year = {2022},
author = {Uzelac, M and Li, Y and Chakladar, J and Li, WT and Ongkeko, WM},
title = {Archaea Microbiome Dysregulated Genes and Pathways as Molecular Targets for Lung Adenocarcinoma and Squamous Cell Carcinoma.},
journal = {International journal of molecular sciences},
volume = {23},
number = {19},
pages = {},
pmid = {36232866},
issn = {1422-0067},
mesh = {*Adenocarcinoma of Lung/pathology ; Archaea/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics ; *Carcinoma, Squamous Cell/pathology ; Female ; Humans ; *Lung Neoplasms/pathology ; Male ; *Microbiota/genetics ; },
abstract = {The human microbiome is a vast collection of microbial species that exist throughout the human body and regulate various bodily functions and phenomena. Of the microbial species that exist in the human microbiome, those within the archaea domain have not been characterized to the extent of those in more common domains, despite their potential for unique metabolic interaction with host cells. Research has correlated tumoral presence of bacterial microbial species to the development and progression of lung cancer; however, the impacts and influences of archaea in the microbiome remain heavily unexplored. Within the United States lung cancer remains highly fatal, responsible for over 100,000 deaths every year with a 5-year survival rate of roughly 22.9%. This project attempts to investigate specific archaeal species' correlation to lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) incidence, patient staging, death rates across individuals of varying ages, races, genders, and smoking-statuses, and potential molecular targets associated with archaea microbiome. Archaeal species abundance was assessed across lung tissue samples of 527 LUAD patients, 479 LUSC patients, and 99 healthy individuals. Nine archaeal species were found to be of significantly altered abundance in cancerous samples as compared to normal counterparts, 6 of which are common to both LUAD and LUSC subgroups. Several of these species are of the taxonomic class Thermoprotei or the phylum Euryarchaeota, both known to contain metabolic processes distinct from most bacterial species. Host-microbe metabolic interactions may be responsible for the observed correlation of these species' abundance with cancer incidence. Significant microbes were correlated to patient gene expression to reveal genes of altered abundance with respect to high and low archaeal presence. With these genes, cellular oncogenic signaling pathways were analyzed for enrichment across cancer and normal samples. In comparing gene expression between LUAD and adjacent normal samples, 2 gene sets were found to be significantly enriched in cancers. In LUSC comparison, 6 sets were significantly enriched in cancer, and 34 were enriched in normals. Microbial counts across healthy and cancerous patients were then used to develop a machine-learning based predictive algorithm, capable of distinguishing lung cancer patients from healthy normal with 99% accuracy.},
}

*Adenocarcinoma of Lung/pathology
Archaea/genetics
*Carcinoma, Non-Small-Cell Lung/genetics
*Carcinoma, Squamous Cell/pathology
Female
Humans
*Lung Neoplasms/pathology
Male
*Microbiota/genetics

@article {pmid36229494,
year = {2022},
author = {Jeter, VL and Schwarzwalder, AH and Rayment, I and Escalante-Semerena, JC},
title = {Structural studies of the phosphoribosyltransferase involved in cobamide biosynthesis in methanogenic archaea and cyanobacteria.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {17175},
pmid = {36229494},
issn = {2045-2322},
support = {R35 GM130399/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Monophosphate ; Archaea/metabolism ; Aspartic Acid ; Cobamides/metabolism ; Crystallography, X-Ray ; *Cyanobacteria/metabolism ; *Euryarchaeota/metabolism ; Glutamates ; Ligands ; Pentosyltransferases/genetics/metabolism ; Phosphates/metabolism ; },
abstract = {Cobamides (Cbas) are coenzymes used by cells across all domains of life, but de novo synthesis is only found in some bacteria and archaea. Five enzymes assemble the nucleotide loop in the alpha phase of the corrin ring. Condensation of the activated ring and nucleobase yields adenosyl-Cba 5'-phosphate, which upon dephosphorylation yields the biologically active coenzyme (AdoCba). Base activation is catalyzed by a phosphoribosyltransferase (PRTase). The structure of the Salmonella enterica PRTase enzyme (i.e., SeCobT) is well-characterized, but archaeal PRTases are not. To gain insights into the mechanism of base activation by the PRTase from Methanocaldococcus jannaschii (MjCobT), we solved crystal structures of the enzyme in complex with substrate and products. We determined several structures: (i) a 2.2 Å structure of MjCobT in the absence of ligand (apo), (ii) structures of MjCobT bound to nicotinate mononucleotide (NaMN) and α-ribazole 5'-phosphate (α-RP) or α-adenylyl-5'-phosphate (α-AMP) at 2.3 and 1.4 Å, respectively. In MjCobT the general base that triggers the reaction is an aspartate residue (Asp 52) rather than a glutamate residue (E317) as in SeCobT. Notably, the dimer interface in MjCobT is completely different from that observed in SeCobT. Finally, entry PDB 3L0Z does not reflect the correct structure of MjCobT.},
}

Adenosine Monophosphate
Archaea/metabolism
Aspartic Acid
Cobamides/metabolism
Crystallography, X-Ray
*Cyanobacteria/metabolism
*Euryarchaeota/metabolism
Glutamates
Ligands
Pentosyltransferases/genetics/metabolism
Phosphates/metabolism

@article {pmid36212815,
year = {2022},
author = {Benito Merino, D and Zehnle, H and Teske, A and Wegener, G},
title = {Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {988871},
pmid = {36212815},
issn = {1664-302X},
abstract = {In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate-methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.},
}

@article {pmid36203131,
year = {2022},
author = {Somee, MR and Amoozegar, MA and Dastgheib, SMM and Shavandi, M and Maman, LG and Bertilsson, S and Mehrshad, M},
title = {Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {690},
pmid = {36203131},
issn = {1471-2164},
mesh = {*Archaea ; Bacteria ; Biodegradation, Environmental ; Carbon/metabolism ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; *Petroleum/metabolism ; Phylogeny ; },
abstract = {BACKGROUND: Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. RESULTS: Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.

CONCLUSION: Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.},
}

*Archaea
Bacteria
Biodegradation, Environmental
Carbon/metabolism
Hydrocarbons/metabolism
Hydrogen/metabolism
*Petroleum/metabolism
Phylogeny

@article {pmid36181435,
year = {2022},
author = {Zhang, X and Huang, Y and Liu, Y and Xu, W and Pan, J and Zheng, X and Du, H and Zhang, C and Lu, Z and Zou, D and Liu, Z and Cai, M and Xiong, J and Zhu, Y and Dong, Z and Jiang, H and Dong, H and Jiang, J and Luo, Z and Huang, L and Li, M},
title = {An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales.},
journal = {Molecular biology and evolution},
volume = {39},
number = {10},
pages = {},
pmid = {36181435},
issn = {1537-1719},
mesh = {*Archaea/genetics/metabolism ; *Hydrogenase/chemistry/genetics/metabolism ; Sodium Chloride/metabolism ; Phylogeny ; Respiratory System/metabolism ; Amino Acids/genetics ; Antiporters/genetics/metabolism ; },
abstract = {Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.},
}

*Archaea/genetics/metabolism
*Hydrogenase/chemistry/genetics/metabolism
Sodium Chloride/metabolism
Phylogeny
Respiratory System/metabolism
Amino Acids/genetics
Antiporters/genetics/metabolism

@article {pmid36160229,
year = {2022},
author = {Meng, K and Chung, CZ and Söll, D and Krahn, N},
title = {Unconventional genetic code systems in archaea.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1007832},
pmid = {36160229},
issn = {1664-302X},
support = {R35 GM122560/GM/NIGMS NIH HHS/United States ; },
abstract = {Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.},
}

@article {pmid36152750,
year = {2022},
author = {Guo, LT and Amikura, K and Jiang, HK and Mukai, T and Fu, X and Wang, YS and O'Donoghue, P and Söll, D and Tharp, JM},
title = {Ancestral archaea expanded the genetic code with pyrrolysine.},
journal = {The Journal of biological chemistry},
volume = {298},
number = {11},
pages = {102521},
pmid = {36152750},
issn = {1083-351X},
support = {K99 GM141320/GM/NIGMS NIH HHS/United States ; R35 GM122560/GM/NIGMS NIH HHS/United States ; 165985//CIHR/Canada ; },
mesh = {*Amino Acyl-tRNA Synthetases/metabolism ; *Archaea/enzymology/genetics ; *Genetic Code ; *Lysine/analogs & derivatives/genetics ; Methanosarcina ; RNA, Transfer/genetics ; },
abstract = {The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA[Pyl]) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA[Pyl] pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA[Pyl] and reveal the emergence of tRNA[Pyl] sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA[Pyl] species with the more common G73-containing tRNA[Pyl] will enable future efforts to engineer PylRS systems for further genetic code expansion.},
}

*Amino Acyl-tRNA Synthetases/metabolism
*Archaea/enzymology/genetics
*Genetic Code
*Lysine/analogs & derivatives/genetics
Methanosarcina
RNA, Transfer/genetics

@article {pmid36150484,
year = {2022},
author = {Guo, Z and Jalalah, M and Alsareii, SA and Harraz, FA and Thakur, N and Salama, ES},
title = {Biochar addition augmented the microbial community and aided the digestion of high-loading slaughterhouse waste: Active enzymes of bacteria and archaea.},
journal = {Chemosphere},
volume = {309},
number = {Pt 1},
pages = {136535},
doi = {10.1016/j.chemosphere.2022.136535},
pmid = {36150484},
issn = {1879-1298},
mesh = {Archaea/metabolism ; Biofuels ; Anaerobiosis ; Bioreactors ; Abattoirs ; Methane/metabolism ; *Hydrogenase/metabolism ; Bacteria/metabolism ; *Microbiota ; Fatty Acids, Volatile/metabolism ; *Lyases/metabolism ; Transaminases ; Digestion ; },
abstract = {The biogas production (BP), volatile fatty acids (VFAs), microbial communities, and microbes' active enzymes were studied upon the addition of biochar (0-1.5%) at 6% and 8% slaughterhouse waste (SHW) loadings. The 0.5% biochar enhanced BP by 1.5- and 1.6-folds in 6% and 8% SHW-loaded reactors, respectively. Increasing the biochar up to 1.5% caused a reduction in BP at 6% SHW. However, the BP from 8% of SHW was enhanced by 1.4-folds at 1.5% biochar. The VFAs production in all 0.5% biochar amended reactors was highly significant compared to control (p-value < 0.05). The biochar addition increased the bacterial and archaeal diversity at both 6% and 8% SHW loadings. The highest number of OTUs at 0.5% biochar were 567 and 525 in 6% and 8% SHW, respectively. Biochar prompted the Clostridium abundance and increased the lyases and transaminases involved in the degradation of lipids and protein, respectively. Biochar addition improved the Methanosaeta and Methanosphaera abundance in which the major enzymes were reductase and hydrogenase. The archaeal enzymes showed mixed acetoclastic and hydrogenotrophic methanogenesis.},
}

Archaea/metabolism
Biofuels
Anaerobiosis
Bioreactors
Abattoirs
Methane/metabolism
*Hydrogenase/metabolism
Bacteria/metabolism
*Microbiota
Fatty Acids, Volatile/metabolism
*Lyases/metabolism
Transaminases
Digestion

@article {pmid36144426,
year = {2022},
author = {Pilotto, S and Werner, F},
title = {How to Shut Down Transcription in Archaea during Virus Infection.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
pmid = {36144426},
issn = {2076-2607},
support = {/WT_/Wellcome Trust/United Kingdom ; 206166/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 202679/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Multisubunit RNA polymerases (RNAPs) carry out transcription in all domains of life; during virus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription with distinct outcomes for different host-virus combinations. These repressors serve as versatile molecular probes to study RNAP mechanisms, as well as aid the exploration of druggable sites for the development of new antibiotics. Here, we review the mechanisms and structural basis of RNAP inhibition by the viral repressor RIP and the crenarchaeal negative regulator TFS4, which follow distinct strategies. RIP operates by occluding the DNA-binding channel and mimicking the initiation factor TFB/TFIIB. RIP binds tightly to the clamp and locks it into one fixed position, thereby preventing conformational oscillations that are critical for RNAP function as it progresses through the transcription cycle. TFS4 engages with RNAP in a similar manner to transcript cleavage factors such as TFS/TFIIS through the NTP-entry channel; TFS4 interferes with the trigger loop and bridge helix within the active site by occlusion and allosteric mechanisms, respectively. The conformational changes in RNAP described above are universally conserved and are also seen in inactive dimers of eukaryotic RNAPI and several inhibited RNAP complexes of both bacterial and eukaryotic RNA polymerases, including inactive states that precede transcription termination. A comparison of target sites and inhibitory mechanisms reveals that proteinaceous repressors and RNAP-specific antibiotics use surprisingly common ways to inhibit RNAP function.},
}

@article {pmid36135934,
year = {2022},
author = {Groult, B and Bredin, P and Lazar, CS},
title = {Ecological processes differ in community assembly of Archaea, Bacteria and Eukaryotes in a biogeographical survey of groundwater habitats in the Quebec region (Canada).},
journal = {Environmental microbiology},
volume = {24},
number = {12},
pages = {5898-5910},
doi = {10.1111/1462-2920.16219},
pmid = {36135934},
issn = {1462-2920},
mesh = {Archaea/genetics ; Eukaryota ; Quebec ; RNA, Ribosomal, 16S ; Bacteria/genetics ; *Groundwater/microbiology ; *Microbiota ; },
abstract = {Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km[2] in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities.},
}

Archaea/genetics
Eukaryota
Quebec
RNA, Ribosomal, 16S
Bacteria/genetics
*Groundwater/microbiology
*Microbiota

@article {pmid36125864,
year = {2022},
author = {Pallen, MJ and Rodriguez-R, LM and Alikhan, NF},
title = {Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.005482},
pmid = {36125864},
issn = {1466-5034},
mesh = {*Archaea/genetics ; Bacteria/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.},
}

*Archaea/genetics
Bacteria/genetics
Bacterial Typing Techniques
Base Composition
DNA, Bacterial/genetics
*Fatty Acids/chemistry
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid36125771,
year = {2022},
author = {Adam, PS and Bornemann, TLV and Probst, AJ},
title = {Progress and Challenges in Studying the Ecophysiology of Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2522},
number = {},
pages = {469-486},
pmid = {36125771},
issn = {1940-6029},
mesh = {Alkanes ; *Archaea/genetics ; *Genome, Archaeal ; Methane ; Phylogeny ; },
abstract = {It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.},
}

Alkanes
*Archaea/genetics
*Genome, Archaeal
Methane
Phylogeny

@article {pmid36125745,
year = {2022},
author = {Thomsen, J and Weidenbach, K and Metcalf, WW and Schmitz, RA},
title = {Genetic Methods and Construction of Chromosomal Mutations in Methanogenic Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2522},
number = {},
pages = {105-117},
pmid = {36125745},
issn = {1940-6029},
mesh = {*Archaea ; *Hypoxanthine Phosphoribosyltransferase/genetics ; Mutation ; Purines ; },
abstract = {Genetic manipulation through markerless exchange enables the modification of several genomic regions without leaving a selection marker in the genome. Here, a method using hpt coding for hypoxanthine phosphoribosyltransferase as a counter selectable marker is described. For Methanosarcina species a chromosomal deletion of the hpt gene is firstly generated, which confers resistance to the purine analogue 8-aza-2,6-diaminopurine (8-ADP). In a second step, the reintroduction of the hpt gene on a plasmid leads to a selectable loss of 8-ADP resistance after a homologous recombination event (pop-in). A subsequent pop-out event restores the 8-ADP resistance and can generate chromosomal mutants with frequencies of about 50%.},
}

*Archaea
*Hypoxanthine Phosphoribosyltransferase/genetics
Mutation
Purines

@article {pmid36125740,
year = {2022},
author = {Forterre, P},
title = {Archaea: A Goldmine for Molecular Biologists and Evolutionists.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2522},
number = {},
pages = {1-21},
pmid = {36125740},
issn = {1940-6029},
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; Eukaryota/genetics ; Genome, Archaeal ; RNA, Ribosomal, 16S ; },
abstract = {The rebuttal of the prokaryote-eukaryote dichotomy and the elaboration of the three domains concept by Carl Woese and colleagues has been a breakthrough in biology. With the methodologies available at this time, they have shown that a single molecule, the 16S ribosomal RNA, could reveal the global organization of the living world. Later on, mining archaeal genomes led to major discoveries in archaeal molecular biology, providing a third model for comparative molecular biology. These analyses revealed the strong eukaryal flavor of the basic molecular fabric of Archaea and support rooting the universal tree between Bacteria and Arcarya (the clade grouping Archaea and Eukarya). However, in contradiction with this conclusion, it remains to understand why the archaeal and bacterial mobilomes are so similar and so different from the eukaryal one. These last years, the number of recognized archaea lineages (phyla?) has exploded. The archaeal nomenclature is now in turmoil and debates about the nature of the last universal common ancestor, the last archaeal common ancestor, and the topology of the tree of life are still going on. Interestingly, the expansion of the archaeal eukaryome, especially in the Asgard archaea, has provided new opportunities to study eukaryogenesis. In recent years, the application to Archaea of the new methodologies described in the various chapters of this book have opened exciting avenues to study the molecular biology and the physiology of these fascinating microorganisms.},
}

*Archaea/genetics
Bacteria/genetics
*Biological Evolution
Eukaryota/genetics
Genome, Archaeal
RNA, Ribosomal, 16S

@article {pmid36125558,
year = {2022},
author = {Chow, C and Padda, KP and Puri, A and Chanway, CP},
title = {An Archaic Approach to a Modern Issue: Endophytic Archaea for Sustainable Agriculture.},
journal = {Current microbiology},
volume = {79},
number = {11},
pages = {322},
pmid = {36125558},
issn = {1432-0991},
mesh = {Agriculture/methods ; Amino Acids/metabolism ; *Archaea/genetics ; *Coffee/metabolism ; Endophytes/genetics/metabolism ; Plant Growth Regulators/metabolism ; Plants ; },
abstract = {Archaea have existed for over 3.5 billion years, yet they were detected in the plant endosphere only in the recent past and still, not much is known about them. Archaeal endophytes may be important microorganisms for sustainable agriculture, particularly in the face of climate change and increasing food demand due to population growth. Recent advances in culture-independent methods of research have revealed a diverse abundance of archaea from the phyla Euryarchaeota, Crenarchaeaota, and Thaumarchaeota globally that are associated with significant crops such as maize, rice, coffee, and olive. Novel insights into the plant microbiome have revealed specific genes in archaea that may be involved in numerous plant metabolic functions including amino acid production and phytohormone modulation. This is the first review article to address what is known about archaea as endophytes, including their patterns of colonization and abundance in various parts of different crop plants grown under diverse environmental conditions. This review aims to facilitate mainstream discussions and encourage future research regarding the occurrence and role of endophytic archaea in plants, particularly in relation to agricultural applications.},
}

Agriculture/methods
Amino Acids/metabolism
*Archaea/genetics
*Coffee/metabolism
Endophytes/genetics/metabolism
Plant Growth Regulators/metabolism
Plants

@article {pmid36111740,
year = {2022},
author = {Yue, Y and Wang, F and Pan, J and Chen, XP and Tang, Y and Yang, Z and Ma, J and Li, M and Yang, M},
title = {Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {11},
pages = {},
doi = {10.1093/femsec/fiac109},
pmid = {36111740},
issn = {1574-6941},
mesh = {*Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Geologic Sediments/chemistry ; Nutrients ; China ; Phylogeny ; DNA, Archaeal/genetics ; },
abstract = {Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.},
}

*Archaea/genetics
RNA, Ribosomal, 16S/genetics
*Ecosystem
Geologic Sediments/chemistry
Nutrients
China
Phylogeny
DNA, Archaeal/genetics

@article {pmid36083447,
year = {2022},
author = {Zhu, Q and Mirarab, S},
title = {Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2569},
number = {},
pages = {137-165},
pmid = {36083447},
issn = {1940-6029},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Software ; },
abstract = {Phylogenomics is the inference of phylogenetic trees based on multiple marker genes sampled in the genomes of interest. An important challenge in phylogenomics is the potential incongruence among the evolutionary histories of individual genes, which can be widespread in microorganisms due to the prevalence of horizontal gene transfer. This protocol introduces the procedures for building a phylogenetic tree of a large number of microbial genomes using a broad sampling of marker genes that are representative of whole-genome evolution. The protocol highlights the use of a gene tree summary method, which can effectively reconstruct the species tree while accounting for the topological conflicts among individual gene trees. The pipeline described in this protocol is scalable to tens of thousands of genomes while retaining high accuracy. We discussed multiple software tools, libraries, and scripts to enable convenient adoption of the protocol. The protocol is suitable for microbiology and microbiome studies based on public genomes and metagenomic data.},
}

*Archaea/genetics
*Bacteria/genetics
Evolution, Molecular
Gene Transfer, Horizontal
Phylogeny
Software

@article {pmid36050385,
year = {2022},
author = {Hoegenauer, C and Hammer, HF and Mahnert, A and Moissl-Eichinger, C},
title = {Methanogenic archaea in the human gastrointestinal tract.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {19},
number = {12},
pages = {805-813},
pmid = {36050385},
issn = {1759-5053},
mesh = {Humans ; *Archaea/physiology ; *Euryarchaeota ; Gastrointestinal Tract/microbiology ; Methane ; Bacteria ; },
abstract = {The human microbiome is strongly interwoven with human health and disease. Besides bacteria, viruses and eukaryotes, numerous archaea are located in the human gastrointestinal tract and are responsible for methane production, which can be measured in clinical methane breath analyses. Methane is an important readout for various diseases, including intestinal methanogen overgrowth. Notably, the archaea responsible for methane production are largely overlooked in human microbiome studies due to their non-bacterial biology and resulting detection issues. As such, their importance for health and disease remains largely unclear to date, in particular as not a single archaeal representative has been deemed to be pathogenic. In this Perspective, we discuss the current knowledge on the clinical relevance of methanogenic archaea. We explain the archaeal unique response to antibiotics and their negative and positive effects on human physiology, and present the current understanding of the use of methane as a diagnostic marker.},
}

Humans
*Archaea/physiology
*Euryarchaeota
Gastrointestinal Tract/microbiology
Methane
Bacteria