• The four archaeal 16S rRNA sequences that were obtained using the poly(A) tailing method formed deeply branching lineages that were related to Candidatus "Parvarchaeum" and the ancient archaeal group. (frontiersin.org)
  • Microbial diversity was determined by 16S ribosomal RNA (rRNA) gene sequencing. (mpg.de)
  • Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. (gtiit.edu.cn)
  • 2] U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops HP, Wagner M. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. (chinagene.cn)
  • Small RNAs involved in rRNA methylation and ribosome biogenesis have been found in Archaea. (biomedcentral.com)
  • Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. (frontiersin.org)
  • The by far most often used marker for prokaryotic diversity studies is the 16S rRNA or its corresponding gene. (frontiersin.org)
  • Restriction fragment length polymorphism analyses of archaeal 16S rRNA genes from seven wells indicated that there were links between archaeal communities and pore water salinity. (umass.edu)
  • Archaeal clone libraries constructed from sequences from 16S rRNA genes isolated from two wells revealed phylotypes similar to a halophilic methylotrophic Methanohalophilus species and a hydrogenotrophic Methanoplanus species at high salinity and a single phylotype closely related to Methanocorpusculum bavaricum at low salinity. (umass.edu)
  • All known archaeal viruses have genomes made of deoxyribonucleic acid (DNA), but some may contain ribonucleic acid (RNA) genomes. (wikipedia.org)
  • To do this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information, and used all annotated and predicted proteins to identify potential protein domains. (mdpi.com)
  • Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. (openwetware.org)
  • Characterization of promoters in archaeal genomes based on DNA structural parameters. (openwetware.org)
  • Satellite viruses replicating in plants have small icosahedral virions and encapsidate positive-sense RNA genomes typically carrying a single gene for the capsid protein. (hal.science)
  • All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas ) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. (biomedcentral.com)
  • For users interested in dsrA/B-based amplicon surveys to study the microbial ecology of dsrAB-encoding sulfate/sulfite reducers or sulfur oxidizers, dsrAB@SILVA provides a curated dsrA and dsrB database accompanied by a GTDB-based taxonomy as based on 902 bacterial and 48 archaeal (metagenome-assambled) genomes. (arb-silva.de)
  • A comparison of library diversity indices indicated that the poly(A) tailing method retrieves more phylogenetically diverse sequences from the environment. (frontiersin.org)
  • The DNA of a mixed community growing at 83°C, pH 7.6, was extracted and the small subunit ribosomal RNA gene (16S rDNA) sequences were obtained using the polymerase chain reaction. (montana.edu)
  • A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
  • Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. (chinagene.cn)
  • jphydit: a java-based integrated environment for molecular phylogeny of ribosomal RNA sequences. (microbiologyresearch.org)
  • Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea . (springer.com)
  • Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. (frontiersin.org)
  • However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. (frontiersin.org)
  • Erko had worked with Carl Woese in pioneering the use of ribosomal RNA sequences to investigate evolutionary relationships among prokaryotes. (ncl.ac.uk)
  • An archaeal virus is a virus that infects and replicates in archaea, a domain of unicellular, prokaryotic organisms. (wikipedia.org)
  • Some environments, such as acidic hot springs, are almost exclusively populated by archaea, so these environments are highly useful for studying how archaeal viruses interact with their hosts. (wikipedia.org)
  • Since 1990, "archaeal virus" has been the dominant term when describing viruses that infect archaea. (wikipedia.org)
  • One of such clades is the Asgard archaea, a deeply-branching archaeal superphylum that currently represents the closest prokaryotic relative of eukaryotes in the Tree of Life (e.g. see Spang et al, Nature 521, 173-178 (2015) & Zaremba -Niedzwiedzka et al. (fems-microbiology.org)
  • The use of molecular phylogenetic approaches in microbial ecology has revolutionized our view of microbial diversity at high temperatures and led to the proposal of a new kingdom within the Archaea, namely, the "Korarchaeota. (montana.edu)
  • Her research interest are biocuration, phylogeny and taxonomy of Bacteria and Archaea, and lastly combining the former two to understand diversity and structure of microbial communities in marine habitats. (unieuk.net)
  • However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. (gtiit.edu.cn)
  • 5] WF, Logsdon JM Jr. Archaeal genomics: do archaea have a mixed heritage? (chinagene.cn)
  • Compared to bacterial and eukaryotic viruses, few archaeal viruses have been described in detail. (wikipedia.org)
  • In general, all archaeal viruses can be placed into two broad groups: those that are related to bacterial and eukaryotic viruses and those that are not. (wikipedia.org)
  • Multiple sequence alignments of MAT genes from a wide diversity of eukaryotes demonstrated a paralogue of MAT, named MATX, with distinctive features that are absent in all other eukaryotic MATs. (biomedcentral.com)
  • Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. (biomedcentral.com)
  • Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and the RNA-dependent RNA polymerase. (biomedcentral.com)
  • There are two major, distinct forms of regulatory small RNAs involved in eukaryotic gene silencing: small interfering (si) RNAs and micro (mi) RNAs. (biomedcentral.com)
  • While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. (uni.lu)
  • In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems. (uni.lu)
  • The diversity of eukaryotic energy metabolism is extremely limited, much narrower than that of prokaryotes. (asmblog.org)
  • Since 2000, methods such as metagenomics have identified many novel archaeal viruses, and methods such as cryogenic electron microscopy and gene synteny have helped to better understand their evolutionary history. (wikipedia.org)
  • or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)
  • High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. (uni.lu)
  • A large portion of the genes encoded by archaeal viruses have no known function or homology to any other genes. (wikipedia.org)
  • Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. (mblwhoilibrary.org)
  • The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. (biomedcentral.com)
  • Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. (biomedcentral.com)
  • The former includes viruses found in the realms Duplodnaviria and Varidnaviria, which likely have ancient origins preceding the LACA, and the latter includes the realm Adnaviria and all archaeal virus families unassigned to higher taxa, which are thought to have more recent origins from non-viral mobile genetic elements such as plasmids. (wikipedia.org)
  • At the stations in the SWIR axial valley (3,655-4,448 m water depth), microbial communities were enriched in bacterial and archaeal taxa common in organic matter-rich subsurface sediments (e.g. (mpg.de)
  • More recently, she has been active in developing hypothesis-specific reference ribosomal RNA datasets, with tailored phylogeny and taxonomy, in order to help answer questions on ecology and function of specific bacterial and archaeal taxa. (unieuk.net)
  • Archaeal viruses, like their hosts, are found worldwide, including in extreme environments inhospitable to most life such as acidic hot springs, highly saline bodies of water, and at the bottom of the ocean. (wikipedia.org)
  • The first known archaeal virus was described in 1974 and since then, a large diversity of archaeal viruses have been discovered, many possessing unique characteristics not found in other viruses. (wikipedia.org)
  • Much of the diversity observed in archaeal viruses is their morphology. (wikipedia.org)
  • How archaeal viruses interact with their hosts and the environment is largely unknown. (wikipedia.org)
  • In oceans, archaeal viruses are believed to play a major role in recycling nutrients, especially at the bottom of the ocean where they are a major cause of death. (wikipedia.org)
  • For some archaeal viruses in hypersaline environments, the level of salinity can affect infectivity and virus behavior. (wikipedia.org)
  • Archaeal viruses were originally referred to as "bacteriophages" or simply "phages", terms shared with bacterial viruses. (wikipedia.org)
  • At around the same time as the adoption of archaebacteria as a name, though, archaeal viruses began to be referred to as viruses, not phages. (wikipedia.org)
  • The trend from "phage" to "virus" when describing archaeal viruses progressed throughout the 1980s. (wikipedia.org)
  • It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. (mdpi.com)
  • This article describes the diversity and properties of these viruses. (hal.science)
  • siRNAs are produced from double-stranded RNAs of viruses and transposable elements, which are processed by the dicer nuclease, one of the essential components of the RNA-Induced Silencing Complexes (RISCs) [ 7 - 9 ]. (biomedcentral.com)
  • ABSTRACT The archaeal diversity in a shallow geothermal well on Vulcano Island, Italy was characterized using culture‐independent 16S rDNA sequence analysis. (sagepub.com)
  • Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. (microbiologyresearch.org)
  • The big picture the deepest divisions of life are very old the ancestors of all current diversity were singlecelled and prokaryotic prokaryotes had evolved by 3. (web.app)
  • The aim of the current project is to employ various genomics strategies to gain insight in the physiology and metabolism of selected Asgard archaeal lineages that reside in anoxic environments. (fems-microbiology.org)
  • The collected genomic, transcriptomic and proteomic datasets will be used to investigate the physiology and genomic activity of Asgard archaeal lineages that reside in anoxic sediments. (fems-microbiology.org)
  • Asgard is a newly proposed archaeal superphylum. (gtiit.edu.cn)
  • Light-activated " Peptide synthesis at the origin of life " links epigenetic effects on protonated RNA interference to God's protection from virus-mediated alterations in microRNAs that enhance virus replication. (rna-mediated.com)
  • This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago. (springer.com)
  • In an attempt to determine which grassland management factors select for particular crenarchaeal community structures, soil microcosm experiments were performed examining the effect of increased pH, application of inorganic fertilizer (ammonium nitrate) and sheep urine deposition on both archaeal and bacterial communities in unmanaged grassland soil. (elsevierpure.com)
  • As grassland management typically increases pH, a further experiment examined the effect of a reduction in pH, to that typical of unimproved grassland soils, on archaeal and bacterial communities. (elsevierpure.com)
  • Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms. (openwetware.org)
  • Dual-species transcriptomics or dual-RNA-seq studies use transcriptomics to assess the transcriptional profiles of multiple organisms originating from the same sample [ 15 ]. (biomedcentral.com)
  • The organisms studied in dual-species transcriptomics experiments are present in different relative abundances and while the read proportions between the two organisms differ by system, most infection models, particularly biologically relevant models, have the total RNA content of the host vastly outnumbering microbe [ 15 ]. (biomedcentral.com)
  • b) Box and whisker plots showing range … Taxonomic Diversity The taxonomic diversity of sequenced marine phages is quite low as compared to the diversity of the sequenced inhibitor Axitinib phages from all habitats (Figure 6). (bcl-2protein.com)
  • The discovery of the elaborate and versatile systems of RNA silencing in eukaryotes is one of the pivotal advances in biology of the last decade [ 1 - 6 ]. (biomedcentral.com)
  • Salinity constraints on subsurface archaeal diversity and methanogenesis in sedimentary rock rich in organic matter. (umass.edu)
  • The diversity of microorganisms active within sedimentary rocks provides important controls on the geochemistry of many subsurface environments. (umass.edu)
  • In this study, archaeal diversity was investigated along a salinity gradient spanning 8 to 3,490 mM Cl(-) in a subsurface shale rich in CH(4) derived from biodegradation of sedimentary hydrocarbons. (umass.edu)
  • these have been investigated mostly by adapting methods used to isolate bacteriophages to the unique growth conditions of their archaeal hosts. (bepress.com)
  • Research areas in archaeal virology include gaining a better understanding of their diversity and learning about their means of replication. (wikipedia.org)
  • The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. (mblwhoilibrary.org)
  • This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA/messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans. (rna-mediated.com)
  • We conclude that ultraslow spreading ridges create a unique environmental setting in sedimented segments without distinct hydrothermal activity, and play an important role in shaping microbial communities and promoting diversity, but also in connectivity among deep-sea habitats. (mpg.de)
  • In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. (frontiersin.org)
  • highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. (biomedcentral.com)
  • In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. (frontiersin.org)
  • However, that the nonbacterial RNase P RNAs retain significant structural similarity to their catalytically active bacterial counterparts indicates that the RNA remains the catalytic center of the enzyme. (colorado.edu)
  • In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. (frontiersin.org)
  • The products were cloned and five different phylogenetic types ("phylotypes") were identified: four archaeal phylotypes, designated pBA1, pBA2, pBA3, and pBA5, and only one bacterial phylotype, designated pBB. (montana.edu)
  • RNase P holoenzymes vary greatly in organizational complexity across the phylogenetic domains, primarily because of differences in the RNase P protein subunits: Mitochondrial, archaeal, and eucaryal holoenzymes contain larger, and perhaps more numerous, protein subunits than do the bacterial holoenzymes. (colorado.edu)
  • This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. (mblwhoilibrary.org)
  • These early discoveries established the value of investigations directed at extremophiles and set the stage for pioneering phylogenetic studies leading to the three-domain view of life and classification of Halobacterium as a member of the archaeal domain. (up.ac.za)
  • Although RNA-only activity has not been demonstrated for the archaeal, eucaryal, or mitochondrial RNAs, comparative sequence analysis has established that these RNAs are homologous (of common ancestry) to bacterial RNA. (colorado.edu)
  • In parallel, the PhD candidate will isolate community RNA and proteins from these sediment layers, which will be analysed using transcriptomics and proteomics approaches. (fems-microbiology.org)
  • This island contains ribosomal proteins or RNA related elements and may indicate a False Positive Prediction! (up.ac.za)
  • While her original environment of interest was the marine water column, and its bacterial and archaeal community, she has diversified her interests to bacterial phyla dominant in soils, biofilm-dwelling Cyanobacteria, and even to fungal biodiversity. (unieuk.net)
  • Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S- and N-rich sections. (mblwhoilibrary.org)
  • Archaeal and eubacterial cells generally lack internal structural organization with a few notable exceptions, like the cyanobacteria. (web.app)
  • Since then, the contribution of the archaeal domain to ecosystem function and diversity was often underestimated in many research fields and studies. (frontiersin.org)
  • The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. (frontiersin.org)
  • A global census of marine microbes Life in the World's Oceans: Diversity, Distribution and Abundance (Vol. " 1 , pp. 223-245). (mbl.edu)
  • It is the process in which the protein is synthesized from the information contained in a molecule of messenger rna mrna. (web.app)
  • Grassland management regimens influence the structure of archaeal communities in upland pasture soils, which appear to be dominated by as yet uncultivated non-thermophilic Crenarchaeota. (elsevierpure.com)
  • Anoxic sediments host a wide diversity of microbial groups that are poorly characterized. (fems-microbiology.org)
  • Since their discovery, extreme halophiles have been studied extensively by chemists, biochemists, microbiologists, and molecular biologists to define both molecular diversity and universal features of life. (up.ac.za)
  • However, metagenomic approaches may not be well-suited to focused studies of microbial diversity and community structure that involve a large number of samples. (frontiersin.org)
  • Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. (frontiersin.org)
  • Viral replication was linked to all pathology in Virus-mediated archaeal hecatomb in the deep seafloor . (rna-mediated.com)
  • The RNA pool tested was extracted from marine sediments of the Yonaguni Knoll IV hydrothermal field in the southern Okinawa Trough. (frontiersin.org)