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Journal articles on the topic 'Evolution of the archaea'

Author: Grafiati

Published: 25 May 2024

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1

Kellner, Siri, Anja Spang, Pierre Offre, Gergely J. Szöllősi, Celine Petitjean, and Tom A. Williams. "Genome size evolution in the Archaea." Emerging Topics in Life Sciences 2, no. 4 (2018): 595–605. http://dx.doi.org/10.1042/etls20180021.

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What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes

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2

Ngcobo, Phelelani Erick, Bridget Valeria Zinhle Nkosi, Wanping Chen, David R. Nelson, and Khajamohiddin Syed. "Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea." International Journal of Molecular Sciences 24, no. 4 (2023): 4161. http://dx.doi.org/10.3390/ijms24044161.

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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

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3

Rafiq, Muhammad, Noor Hassan, Maliha Rehman, et al. "Challenges and Approaches of Culturing the Unculturable Archaea." Biology 12, no. 12 (2023): 1499. http://dx.doi.org/10.3390/biology12121499.

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Since Carl Woese’s discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cu

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4

Gribaldo, Simonetta, and Celine Brochier-Armanet. "The origin and evolution of Archaea: a state of the art." Philosophical Transactions of the Royal Society B: Biological Sciences 361, no. 1470 (2006): 1007–22. http://dx.doi.org/10.1098/rstb.2006.1841.

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Environmental surveys indicate that the Archaea are diverse and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the planet. Archaea display unique capacities, such as methanogenesis and survival at temperatures higher than 90 °C, that make them crucial for understanding the nature of the biota of early Earth. Molecular, genomics and phylogenetics data strengthen Woese's definition of Archaea as a third domain of life in addition to Bacteria and Eukarya. Phylogenomics analyses of the components

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5

Williams, Tom A., Gergely J. Szöllősi, Anja Spang, et al. "Integrative modeling of gene and genome evolution roots the archaeal tree of life." Proceedings of the National Academy of Sciences 114, no. 23 (2017): E4602—E4611. http://dx.doi.org/10.1073/pnas.1618463114.

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A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplicati

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6

Forterre, Patrick. "The Common Ancestor of Archaea and Eukarya Was Not an Archaeon." Archaea 2013 (2013): 1–18. http://dx.doi.org/10.1155/2013/372396.

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It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ances

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7

VERHEES, Corné H., Servé W. M. KENGEN, Judith E. TUININGA, et al. "The unique features of glycolytic pathways in Archaea." Biochemical Journal 375, no. 2 (2003): 231–46. http://dx.doi.org/10.1042/bj20021472.

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An early divergence in evolution has resulted in two prokaryotic domains, the Bacteria and the Archaea. Whereas the central metabolic routes of bacteria and eukaryotes are generally well-conserved, variant pathways have developed in Archaea involving several novel enzymes with a distinct control. A spectacular example of convergent evolution concerns the glucose-degrading pathways of saccharolytic archaea. The identification, characterization and comparison of the glycolytic enzymes of a variety of phylogenetic lineages have revealed a mosaic of canonical and novel enzymes in the archaeal vari

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8

Zhu, Pengfei, Jialin Hou, Yixuan Xiong, Ruize Xie, Yinzhao Wang, and Fengping Wang. "Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis." Microorganisms 12, no. 4 (2024): 707. http://dx.doi.org/10.3390/microorganisms12040707.

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Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway,

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9

Tamarit, Daniel, Eva F. Caceres, Mart Krupovic, et al. "A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses." Nature Microbiology 7, no. 7 (2022): 948–52. http://dx.doi.org/10.1038/s41564-022-01122-y.

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AbstractAsgard archaea have recently been identified as the closest archaeal relatives of eukaryotes. Their ecology, and particularly their virome, remain enigmatic. We reassembled and closed the chromosome of Candidatus Odinarchaeum yellowstonii LCB_4, through long-range PCR, revealing CRISPR spacers targeting viral contigs. We found related viruses in the genomes of diverse prokaryotes from geothermal environments, including other Asgard archaea. These viruses open research avenues into the ecology and evolution of Asgard archaea.

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10

Fouqueau, Thomas, Fabian Blombach, Gwenny Cackett, et al. "The cutting edge of archaeal transcription." Emerging Topics in Life Sciences 2, no. 4 (2018): 517–33. http://dx.doi.org/10.1042/etls20180014.

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The archaeal RNA polymerase (RNAP) is a double-psi β-barrel enzyme closely related to eukaryotic RNAPII in terms of subunit composition and architecture, promoter elements and basal transcription factors required for the initiation and elongation phase of transcription. Understanding archaeal transcription is, therefore, key to delineate the universally conserved fundamental mechanisms of transcription as well as the evolution of the archaeo-eukaryotic transcription machineries. The dynamic interplay between RNAP subunits, transcription factors and nucleic acids dictates the activity of RNAP a

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11

van Passel, M. W. J., C. S. Smillie, and H. Ochman. "Gene decay in archaea." Archaea 2, no. 2 (2007): 137–43. http://dx.doi.org/10.1155/2007/165723.

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The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pse

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12

Lee, Dong-Hun, Jung-Hyun Kim, Yung Mi Lee, et al. "Biogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort Sea." Biogeosciences 15, no. 24 (2018): 7419–33. http://dx.doi.org/10.5194/bg-15-7419-2018.

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Abstract. In this study, we report lipid biomarker patterns and phylogenetic identities of key microbial communities mediating anaerobic oxidation of methane (AOM) in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. The carbon isotopic compositions (δ13C) of sn-2- and sn-3-hydroxyarchaeol showed the highly 13C-depleted values (−114 ‰ to −82 ‰) associated with a steep depletion in sulfate concentrations within 0.7 m of sediment depths. This suggested the presence of methanotrophic archaea involved in sulfate-dependent AOM, albeit in a small amount. The ratio of

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13

Nishida, Hiromi. "Comparative Analyses of Base Compositions, DNA Sizes, and Dinucleotide Frequency Profiles in Archaeal and Bacterial Chromosomes and Plasmids." International Journal of Evolutionary Biology 2012 (March 26, 2012): 1–5. http://dx.doi.org/10.1155/2012/342482.

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In the present paper, I compared guanine-cytosine (GC) contents, DNA sizes, and dinucleotide frequency profiles in 109 archaeal chromosomes, 59 archaeal plasmids, 1379 bacterial chromosomes, and 854 bacterial plasmids. In more than 80% of archaeal and bacterial plasmids, the GC content was lower than that of the host chromosome. Furthermore, most of the differences in GC content found between a plasmid and its host chromosome were less than 10%, and the GC content in plasmids and host chromosomes was highly correlated (Pearson’s correlation coefficient in bacteria and 0.917 in archaea). These

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14

Long, Xi, Hong Xue, and J. Tze-Fei Wong. "Descent of Bacteria and Eukarya From an Archaeal Root of Life." Evolutionary Bioinformatics 16 (January 2020): 117693432090826. http://dx.doi.org/10.1177/1176934320908267.

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The 3 biological domains delineated based on small subunit ribosomal RNAs (SSU rRNAs) are confronted by uncertainties regarding the relationship between Archaea and Bacteria, and the origin of Eukarya. The similarities between the paralogous valyl-tRNA and isoleucyl-tRNA synthetases in 5398 species estimated by BLASTP, which decreased from Archaea to Bacteria and further to Eukarya, were consistent with vertical gene transmission from an archaeal root of life close to Methanopyrus kandleri through a Primitive Archaea Cluster to an Ancestral Bacteria Cluster, and to Eukarya. The predominant sim

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15

Forterre, Patrick, Celine Brochier, and Hervé Philippe. "Evolution of the Archaea." Theoretical Population Biology 61, no. 4 (2002): 409–22. http://dx.doi.org/10.1006/tpbi.2002.1592.

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16

Wang, Yinzhao, Gunter Wegener, Tom A. Williams, et al. "A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism." Science Advances 7, no. 27 (2021): eabj1453. http://dx.doi.org/10.1126/sciadv.abj1453.

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Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide–reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaer

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17

De Lise, Federica, Roberta Iacono, Marco Moracci, Andrea Strazzulli, and Beatrice Cobucci-Ponzano. "Archaea as a Model System for Molecular Biology and Biotechnology." Biomolecules 13, no. 1 (2023): 114. http://dx.doi.org/10.3390/biom13010114.

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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 replicat

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18

Rother, Michael, and Joseph A. Krzycki. "Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea." Archaea 2010 (2010): 1–14. http://dx.doi.org/10.1155/2010/453642.

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Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. Thi

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19

Brueckner, Julia, and William F. Martin. "Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes." Genome Biology and Evolution 12, no. 4 (2020): 282–92. http://dx.doi.org/10.1093/gbe/evaa047.

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Abstract Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes th

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Béjà, Oded, Eugene V. Koonin, L. Aravind, et al. "Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces." Applied and Environmental Microbiology 68, no. 1 (2002): 335–45. http://dx.doi.org/10.1128/aem.68.1.335-345.2002.

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ABSTRACT Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in

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Frohn, Béla P., Tobias Härtel, Jürgen Cox, and Petra Schwille. "Tracing back variations in archaeal ESCRT-based cell division to protein domain architectures." PLOS ONE 17, no. 3 (2022): e0266395. http://dx.doi.org/10.1371/journal.pone.0266395.

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The Endosomal Sorting Complex Required for Transport (ESCRT) system is a multi-protein machinery that is involved in cell division of both Eukaryotes and Archaea. This spread across domains of life suggests that a precursor ESCRT machinery existed already at an evolutionary early stage of life, making it a promising candidate for the (re)construction of a minimal cell division machinery. There are, however, only few experimental data about ESCRT machineries in Archaea, due to high technical challenges in cultivation and microscopy. Here, we analyse the proteins of ESCRT machineries in archaea

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22

Schiraldi, Chiara, Mariateresa Giuliano, and Mario De Rosa. "Perspectives on biotechnological applications of archaea." Archaea 1, no. 2 (2002): 75–86. http://dx.doi.org/10.1155/2002/436561.

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Many archaea colonize extreme environments. They include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. Because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. Despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. This review summarizes current knowledge about the biotechnological uses of archaea and archaeal enzymes with special attention to potential applications that are

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23

Lemmens, Liesbeth, Rani Baes, and Eveline Peeters. "Heat shock response in archaea." Emerging Topics in Life Sciences 2, no. 4 (2018): 581–93. http://dx.doi.org/10.1042/etls20180024.

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An adequate response to a sudden temperature rise is crucial for cellular fitness and survival. While heat shock response (HSR) is well described in bacteria and eukaryotes, much less information is available for archaea, of which many characterized species are extremophiles thriving in habitats typified by large temperature gradients. Here, we describe known molecular aspects of archaeal heat shock proteins (HSPs) as key components of the protein homeostasis machinery and place this in a phylogenetic perspective with respect to bacterial and eukaryotic HSPs. Particular emphasis is placed on s

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Lang, Xiu-lu, Xiang Chen, Ai-ling Xu, Zhi-wen Song, Xin Wang, and He-bing Wang. "Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment." Archaea 2018 (October 16, 2018): 1–12. http://dx.doi.org/10.1155/2018/9319345.

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Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Prot

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Ohene-Adjei, Samuel, Ronald M. Teather, Michael Ivan, and Robert J. Forster. "Postinoculation Protozoan Establishment and Association Patterns of Methanogenic Archaea in the Ovine Rumen." Applied and Environmental Microbiology 73, no. 14 (2007): 4609–18. http://dx.doi.org/10.1128/aem.02687-06.

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ABSTRACT Association patterns between archaea and rumen protozoa were evaluated by analyzing archaeal 16S rRNA gene clone libraries from ovine rumen inoculated with different protozoa. Five protozoan inoculation treatments, fauna free (negative control), holotrich and cellulolytic protozoa, Isotricha and Dasytricha spp., Entodinium spp., and total fauna (type A) were tested. We used denaturing gradient gel electrophoresis, quantitative PCR, and phylogenetic analysis to evaluate the impact of the protozoan inoculants on the respective archaeal communities. Protozoan 18S ribosomal DNA clone libr

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Oost, John van der. "How the Archaea live: Unique features of archaeal metabolism." Biochemist 26, no. 3 (2004): 7–10. http://dx.doi.org/10.1042/bio02603007.

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A major scientific milestone was Carl Woese's discovery that the evolution of life on Earth has resulted in three distinct types of living systems:Archaea, Bacteria and Eukarya1. Organisms that belong to the eukaryal domain are clearly different from the former two because of their more complex structural organization: without exception, they possess intracellular compartments (at least a nucleus, often with additional organelles), and in addition they often have a multicellular composition. The Archaea and the Bacteria are prokaryotes: they have neither a nucleus nor any other cytoplasmic com

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Hartman, Hyman, Paola Favaretto, and Temple F. Smith. "The archaeal origins of the eukaryotic translational system." Archaea 2, no. 1 (2006): 1–9. http://dx.doi.org/10.1155/2006/431618.

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Among the 78 eukaryotic ribosomal proteins, eleven are specific to Eukarya, 33 are common only to Archaea and Eukarya and 34 are homologous (at least in part) to those of both Bacteria and Archaea. Several other translational proteins are common only to Eukarya and Archaea (e.g., IF2a, SRP19, etc.), whereas others are shared by the three phyla (e.g., EFTu/EF1A and SRP54).Although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translational machinery, especially the ribosomal proteins, there have been numerous unique and ubiquitous addit

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Liao, Yan, Solenne Ithurbide, Roshali T. de Silva, Susanne Erdmann, and Iain G. Duggin. "Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope." Emerging Topics in Life Sciences 2, no. 4 (2018): 547–59. http://dx.doi.org/10.1042/etls20180026.

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The tubulin superfamily of cytoskeletal proteins is widespread in all three domains of life — Archaea, Bacteria and Eukarya. Tubulins build the microtubules of the eukaryotic cytoskeleton, whereas members of the homologous FtsZ family construct the division ring in prokaryotes and some eukaryotic organelles. Their functions are relatively poorly understood in archaea, yet these microbes contain a remarkable diversity of tubulin superfamily proteins, including FtsZ for division, a newly described major family called CetZ that is involved in archaeal cell shape control, and several other diverge

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Hamerly, Timothy, Brian Tripet, Louie Wurch, et al. "Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR." Archaea 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/472726.

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Lipids composed of condensed isoprenyl units connected to glycerol backbones by ether linkages are a distinguishing feature of Archaea. Data suggesting that fatty acids with linear hydrocarbon chains are present in some Archaea have been available for decades. However, lack of genomic and biochemical evidence for the metabolic machinery required to synthesize and degrade fatty acids has left the field unclear on this potentially significant biochemical aspect. Because lipids are energy currency and cell signaling molecules, their presence in Archaea is significant for understanding archaeal bi

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Rusch, Antje. "Molecular Tools for the Detection of Nitrogen Cycling Archaea." Archaea 2013 (2013): 1–10. http://dx.doi.org/10.1155/2013/676450.

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Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems. The detection, characterization, and quantification of archaeal functions in mixed communities require Archaea-specific primers or probes for the corresponding metabolic genes. Five pairs of degenerate primers were designed to target archaeal genes encoding key enzymes of nitrogen cycling: nitrite reductases NirA and NirB, nitrous oxide reductase (NosZ), nitrogenase r

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Yoshinaga, Marcos Y., Lars Wörmer, Marcus Elvert, and Kai-Uwe Hinrichs. "Novel Cardiolipins from Uncultured Methane-Metabolizing Archaea." Archaea 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/832097.

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Novel cardiolipins from Archaea were detected by screening the intact polar lipid (IPL) composition of microbial communities associated with methane seepage in deep-sea sediments from the Pakistan margin by high-performance liquid chromatography electrospray ionization mass spectrometry. A series of tentatively identified cardiolipin analogues (dimeric phospholipids or bisphosphatidylglycerol, BPG) represented 0.5% to 5% of total archaeal IPLs. These molecules are similar to the recently described cardiolipin analogues with four phytanyl chains from extreme halophilic archaea. It is worth noti

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Raymann, Kasie, Céline Brochier-Armanet, and Simonetta Gribaldo. "The two-domain tree of life is linked to a new root for the Archaea." Proceedings of the National Academy of Sciences 112, no. 21 (2015): 6670–75. http://dx.doi.org/10.1073/pnas.1420858112.

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One of the most fundamental questions in evolutionary biology is the origin of the lineage leading to eukaryotes. Recent phylogenomic analyses have indicated an emergence of eukaryotes from within the radiation of modern Archaea and specifically from a group comprising Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Crenarchaeota/Korarchaeota (TACK). Despite their major implications, these studies were all based on the reconstruction of universal trees and left the exact placement of eukaryotes with respect to the TACK lineage unclear. Here we have applied an original two-step approach that i

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Navarro-Noya, Yendi E., César Valenzuela-Encinas, Alonso Sandoval-Yuriar, Norma G. Jiménez-Bueno, Rodolfo Marsch, and Luc Dendooven. "Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil." Archaea 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/646820.

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In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic CandidatusNitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family.

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Gunbin, K. V., V. V. Suslov, and D. A. Afonnikov. "Phylogenetic analysis of housekeeping Archaeal proteins and early stages of Archaea evolution." Paleontological Journal 47, no. 9 (2013): 1041–47. http://dx.doi.org/10.1134/s0031030113090098.

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Cowie, Rebecca O. M., Elizabeth W. Maas, and Ken G. Ryan. "Archaeal diversity revealed in Antarctic sea ice." Antarctic Science 23, no. 6 (2011): 531–36. http://dx.doi.org/10.1017/s0954102011000368.

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AbstractArchaea, once thought to be only extremophiles, are now known to be abundant in most environments. They can predominate in microbial communities and be significantly involved in many global biogeochemical cycles. However, Archaea have not been reported in Antarctic sea ice. Our understanding of the ecology of Antarctic sea ice prokaryotes is still in its infancy but this information is important if we are to understand their diversity, adaptations and biogeochemical roles in Antarctic systems. We detected Archaea in sea ice at two sampling sites taken from three subsequent years using

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Lazar, Cassandre Sara, Wenke Stoll, Robert Lehmann, et al. "Archaeal Diversity and CO2Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems." Archaea 2017 (2017): 1–13. http://dx.doi.org/10.1155/2017/2136287.

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Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few sur

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Giaquinto, Laura, Paul M. G. Curmi, Khawar S. Siddiqui, et al. "Structure and Function of Cold Shock Proteins in Archaea." Journal of Bacteriology 189, no. 15 (2007): 5738–48. http://dx.doi.org/10.1128/jb.00395-07.

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ABSTRACT Archaea are abundant and drive critical microbial processes in the Earth's cold biosphere. Despite this, not enough is known about the molecular mechanisms of cold adaptation and no biochemical studies have been performed on stenopsychrophilic archaea (e.g., Methanogenium frigidum). This study examined the structural and functional properties of cold shock proteins (Csps) from archaea, including biochemical analysis of the Csp from M. frigidum. csp genes are present in most bacteria and some eucarya but absent from most archaeal genome sequences, most notably, those of all archaeal th

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Baquero, Diana P., Anastasia D. Gazi, Martin Sachse, et al. "A filamentous archaeal virus is enveloped inside the cell and released through pyramidal portals." Proceedings of the National Academy of Sciences 118, no. 32 (2021): e2105540118. http://dx.doi.org/10.1073/pnas.2105540118.

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The majority of viruses infecting hyperthermophilic archaea display unique virion architectures and are evolutionarily unrelated to viruses of bacteria and eukaryotes. The lack of relationships to other known viruses suggests that the mechanisms of virus–host interaction in Archaea are also likely to be distinct. To gain insights into archaeal virus–host interactions, we studied the life cycle of the enveloped, ∼2-μm-long Sulfolobus islandicus filamentous virus (SIFV), a member of the family Lipothrixviridae infecting a hyperthermophilic and acidophilic archaeon Saccharolobus islandicus LAL14/

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Tirumalai, Madhan R., Raghavan V. Sivaraman, Layla A. Kutty, Eric L. Song, and George E. Fox. "Ribosomal Protein Cluster Organization in Asgard Archaea." Archaea 2023 (September 29, 2023): 1–16. http://dx.doi.org/10.1155/2023/5512414.

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It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an op

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Lorentzen, E., B. Siebers, R. Hensel, and E. Pohl. "Structure, function and evolution of the Archaeal class I fructose-1,6-bisphosphate aldolase." Biochemical Society Transactions 32, no. 2 (2004): 259–63. http://dx.doi.org/10.1042/bst0320259.

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FBPA (fructose-1,6-bisphosphate aldolase) catalyses the reversible aldol condensation of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate to form fructose 1,6-bisphosphate. Two classes of FBPA, which rely on different reaction mechanisms, have so far been discovered, class I mainly found in Eucarya and class II mainly in Bacteria. Only recently were genes encoding proteins with FBPA activity identified in Archaea. Archaeal FBPAs do not share any significant overall sequence identity with members of the traditional classes of FBPAs, raising the interesting question of whether they have

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Soares, Laís Américo, André Cordeiro Alves Dos Santos, Iolanda Cristina Silveira Duarte, Emiliana Manesco Romagnoli, and Maria do Carmo Calijuri. "Distribution of Archaeal and Bacterial communities in a subtropical reservoir." Acta Limnologica Brasiliensia 27, no. 4 (2015): 411–20. http://dx.doi.org/10.1590/s2179-975x3615.

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Abstract Aim: Microbial communities play a central role in environmental process such as organic matter mineralization and the nutrient cycling process in aquatic ecosystems. Despite their ecological importance, variability of the structure of archaeal and bacterial communities in freshwater remains understudied. Methods In the present study we investigated the richness and density of archaea and bacteria in the water column and sediments of the Itupararanga Reservoir. We also evaluated the relationship between the communities and the biotic and abiotic characteristics. Samples were taken at f

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Spang, Anja, Joran Martijn, Jimmy H. Saw, Anders E. Lind, Lionel Guy, and Thijs J. G. Ettema. "Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution." Archaea 2013 (2013): 1–12. http://dx.doi.org/10.1155/2013/202358.

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The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of lif

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Peeters, Eveline, and Daniel Charlier. "The Lrp Family of Transcription Regulators in Archaea." Archaea 2010 (2010): 1–10. http://dx.doi.org/10.1155/2010/750457.

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Archaea possess a eukaryotic-type basal transcription apparatus that is regulated by bacteria-like transcription regulators. A universal and abundant family of transcription regulators are the bacterial/archaeal Lrp-like regulators. The Lrp family is one of the best studied regulator families in archaea, illustrated by investigations of proteins from the archaeal model organisms:Sulfolobus,Pyrococcus,Methanocaldococcus, andHalobacterium. These regulators are extremely versatile in their DNA-binding properties, response to effector molecules, and molecular regulatory mechanisms. Besides being i

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Yip, W. S. Vincent, Nicholas G. Vincent, and Susan J. Baserga. "Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification." Archaea 2013 (2013): 1–14. http://dx.doi.org/10.1155/2013/614735.

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Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome bio

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Shin, David S., Ashley J. Pratt, and John A. Tainer. "Archaeal Genome Guardians Give Insights into Eukaryotic DNA Replication and Damage Response Proteins." Archaea 2014 (2014): 1–24. http://dx.doi.org/10.1155/2014/206735.

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As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the bio

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Baker, Brett J., Valerie De Anda, Kiley W. Seitz, Nina Dombrowski, Alyson E. Santoro, and Karen G. Lloyd. "Diversity, ecology and evolution of Archaea." Nature Microbiology 5, no. 7 (2020): 887–900. http://dx.doi.org/10.1038/s41564-020-0715-z.

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Klenk, Hans-Peter, and W. Ford Doolittle. "Evolution: Archaea and eukaryotes versus bacteria?" Current Biology 4, no. 10 (1994): 920–22. http://dx.doi.org/10.1016/s0960-9822(00)00206-2.

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Besseling, Marc A., Ellen C. Hopmans, R. Christine Boschman, Jaap S. Sinninghe Damsté, and Laura Villanueva. "Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone." Biogeosciences 15, no. 13 (2018): 4047–64. http://dx.doi.org/10.5194/bg-15-4047-2018.

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Abstract. Benthic archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Recent genomic surveys suggest they are largely involved in anaerobic processing of organic matter, but the distribution and abundance of these archaeal groups are still largely unknown. Archaeal membrane lipids composed of isoprenoid diethers or tetraethers (glycerol dibiphytanyl glycerol tetraether, GDGT) are often used as archaeal biomarkers. Here, we compare the archaeal diversity and intact polar lipid (IPL) composition in both surface (0–0.5 cm) and subsurface (10–12 cm) sediments

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Harish, Ajith. "What is an archaeon and are the Archaea really unique?" PeerJ 6 (October 18, 2018): e5770. http://dx.doi.org/10.7717/peerj.5770.

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The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (

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Cabello, Purificación, M. Dolores Roldán, and Conrado Moreno-Vivián. "Nitrate reduction and the nitrogen cycle in archaea." Microbiology 150, no. 11 (2004): 3527–46. http://dx.doi.org/10.1099/mic.0.27303-0.

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The nitrogen cycle (N-cycle) in the biosphere, mainly driven by prokaryotes, involves different reductive or oxidative reactions used either for assimilatory purposes or in respiratory processes for energy conservation. As the N-cycle has important agricultural and environmental implications, bacterial nitrogen metabolism has become a major research topic in recent years. Archaea are able to perform different reductive pathways of the N-cycle, including both assimilatory processes, such as nitrate assimilation and N2 fixation, and dissimilatory reactions, such as nitrate respiration and denitr

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