GenomesArchaeaEukaryotesPhylogeneticMicrobialTaxaGenomicDeeply rootedPlastidMetabolicGenesAnaerobicAbundantEcological and evolutionaryTaxonomicallyDistinctPredominanceClosely relatedPhylaSulfurSpeciesSequencesEnvironmentsViralSequenceBacteriaPhylumDynamicsStructuresBiogeochemicalOrganismsMarineDiverseRepresentsCommunitiesUnknownIndividualSpecificCommonCellsLifeSimilar
Genomes14
- Future determinations of the unbiased mutation rate of more representative lineages with highly reduced genomes such as Prochlorococcus and Pelagibacterales that dominate marine microbial communities are essential to test these hypotheses. (nature.com)
- Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. (darkenergybiosphere.org)
- Discovery of new bacterial species shows little sign of abating, demonstrating the continued need to improve the experimental methods and informatics tooling used to produce metagenome assembled genomes (MAGs) thereby allowing the full microbial diversity to be described. (researchsquare.com)
- which is found in almost all organisms and which sometimes contains operon structures in bacterial genomes. (easyomics.org)
- The first large-scale recovery of thousands of microbial genomes from diverse microbial lineages from metagenomes. (edu.au)
- 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)
- We identify DJR viruses in the genomes of diverse major bacterial and archaeal phyla, and in marine water column and sediment metagenomes, and find that their diversity greatly exceeds the diversity that is currently captured by the three recognized families of such viruses. (elsevierpure.com)
- Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages ( 12 - 14 ) and the discovery of a previously unknown reassignment of TGA opal stop codons to glycine ( 4 , 5 , 14 ). (scienceintheclassroom.org)
- Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off Costa Rica margin, defining a novel lineage phylogenetically married to Thorarchaeota, as such we propose the name "Sifarchaeota" for this phylum. (uibk.ac.at)
- Representative genomes of the "Sifarchaeota" showed remarkable saccharolytic capacities extending the known metabolic features encoded by the Asgard lineages. (uibk.ac.at)
- Results We simulated the stochastic process of gene-loss using the pooled genome-scale metabolic reaction networks of 46 taxonomically diverse bacterial and archaeal families as proxies for their pan-genomes. (springernature.com)
- The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. (biomedcentral.com)
- Through the process of binning, contigs or scaffolds derived from the same lineage can be clustered and genomes reconstructed. (biomedcentral.com)
- The authors stated, 'The number of myosin genes varies markedly between lineages [types of eukaryotes],' and 'holozoan genomes, as well as some amoebozoans and heterokonts, have the highest numbers of myosins of all eukaryotes. (icr.org)
Archaea5
- Overall, these data suggest that viruses of the non-tailed dsDNA DJR lineage are important but often overlooked predators of bacteria and archaea that impose fundamentally different predation and gene transfer regimes on microbial systems than on tailed viruses, which form the basis of all environmental models of bacteria-virus interactions. (elsevierpure.com)
- The comparison of metabolic potentials of the Asgard archaea can help inform about selective pressures the lineages have faced during evolution. (uibk.ac.at)
- Highly divergent lineages of Archaea, unique to South African deep subsurface fracture fluids, are also described. (princeton.edu)
- Whilst archaea have eukaryal-type informational pathways such as DNA replication and transcription, archaeal DNA repair pathways are still poorly understood. (biomedcentral.com)
- While Archaea were once thought to be extremophiles, we now know that one lineage, nitrifying Marine Group I (or Thaumarchaea), numerically dominate below 200m in the ocean. (nature.com)
Eukaryotes2
- Unlike cells of animals and other eukaryotes , bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles . (alchetron.com)
- Archaeal information processing pathways resemble those in eukaryotes, but archaeal damage response pathways remain poorly understood. (biomedcentral.com)
Phylogenetic5
- Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. (bestitservice.be)
- Phylogenetic analysis revealed that NM-R3 belongs to a distinct phylogenetic lineage quite distant from archaeal inward Cl - -pumping rhodopsins like halorhodopsin, suggesting that different types of chloride-pumping rhodopsins have evolved independently within marine bacterial lineages. (elsevierpure.com)
- The distribution of phosphofructokinase (PFK) phosphoryl donor subtypes [ATP-, ADP- and pyrophosphate (PPᵢ)] in the deeply rooted phylogenetic lineages of thermophiles is of interest with respect to the evolution of PFK activity and of the Embden-Meyerhof (EM) pathway. (waikato.ac.nz)
- Sequence analysis and a phylogenetic comparison suggest that the Dictyoglomus PPᵢ-PFK represents an ancient lineage and is closely related to those PPᵢPFKѕ from the archaeal Thermoproteus tenax, bacterial Mycobacterium tuberculosis and Amycolatopsis methanolica, and the ATP-PFK from Streptomyces coelicolor, all of which belong to group III PFKѕ. (waikato.ac.nz)
- 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)
Microbial5
- We showed that genome size is negatively correlated with mutation rate and positively correlated with effective population size across 30 bacterial and archaeal lineages, suggesting that increased mutation rate and random genetic drift are likely two important mechanisms driving microbial genome reduction. (nature.com)
- The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. (nsf.gov)
- A bonanza of novel microbial lineages have been identified in recent years and we are currently challenged with how to phylogenetically and functionally characterize this novel diversity. (doe.gov)
- Moving from cataloging microbial diversity to experimental characterization and validation of the functional potential of these new lineages will provide new cornerstones for research in the areas of bioenergy and biomedicine, as well as biotechnology. (doe.gov)
- Borehole fluids derived from deep fractures were populated by microbial communities with low diversity with an average of 11 and 5 bacterial and archaeal OTUs respectively. (princeton.edu)
Taxa2
- Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. (bestitservice.be)
- They explained it by 1) convergence (the sudden and simultaneous appearance of a gene with no evolutionary patterns in different taxa), 2) lineage-specific expansions (different myosin gene complements found in different creatures), and 3) gene losses (missing genes that evolutionists thought should have been there). (icr.org)
Genomic3
- Comparative genomic analysis based on the full metabolic profiles of Asgard lineages revealed the close relation between "Sifarchaeota" and Odinarchaeota MAGs, which suggested a similar metabolic potentials and ecological roles. (uibk.ac.at)
- By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages. (springernature.com)
- The continued evolution of Omicron lineages highlights the importance of genomic surveillance to monitor emerging variants and help guide vaccine development and use of therapeutics. (cdc.gov)
Deeply rooted1
- We report here the occurrence of another member of this archaeal group and a deeply rooted bacterial sequence from a thermal spring in Yellowstone National Park (USA). (montana.edu)
Plastid2
- The plastid acquisition of a bacterial rpl36 gene via HGT provides the first strong evidence for a sister-group relationship between haptophyte and cryptophyte plastids to the exclusion of heterokont and alveolate plastids. (biomedcentral.com)
- Moreover, the bacterial gene has replaced the native plastid rpl36 gene by an uncertain mechanism that appears inconsistent with existing models for the recombinational basis of gene conversion. (biomedcentral.com)
Metabolic2
- Results imply that certain bacterial and archaeal lineages harbor different population structures and metabolic potentials for colonizing diverse hot spring environments. (bvsalud.org)
- Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets. (springernature.com)
Genes4
- 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)
- Modern smartphones have operating systems, which are like bacterial core genes needed for basic functionality and shared by all the recent phones from a manufacturer. (springernature.com)
- But also have "optional" apps, which are like bacterial accessory genes, providing additional functionality and personalized user experience. (springernature.com)
- Specifically, the ideas of convergent evolution and lineage-specific expansions are nothing more than fancy terms for the fact that these different types of myosin genes appeared suddenly in unrelated creatures at the same time. (icr.org)
Anaerobic3
- Deep-sea hydrothermal vents resemble the early Earth, and thus the dominant Thermococcaceae inhabitants, which occupy an evolutionarily basal position of the archaeal tree and take an obligate anaerobic hyperthermophilic free-living lifestyle, are likely excellent models to study the evolution of early life. (nature.com)
- Haroon MF, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, Yuan Z, Tyson GW (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. (edu.au)
- The same sediments contained abundant 13C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. (mblwhoilibrary.org)
Abundant2
- Eight archaeal and bacterial ASVs from Thermoplasmatales, Desulfurellaceae, Mesoaciditogaceae and Acidithiobacillaceae were unusually prevalent (present in 57.9-84.2% of samples) and abundant (1.7-12.0% sample relative abundance), and together comprised 44% of overall community abundance. (bvsalud.org)
- Prior to joining the JGI in 2010, he made the first ever measurements of in situ growth rates and carbon consumption of SAR11 bacteria, the most abundant bacterial group in the ocean. (doe.gov)
Ecological and evolutionary1
- Furthermore, we identified multiple potential horizontal gene transfer (HGT) events from different bacterial donors within "Sifarchaetoa" MAGs, which hypothetically expanded "Sifarchaeota" capacities for substrate utilization, energy production and niche adaptation.ImportanceDeep marine sediments are the home of multiple poorly described archaeal lineages, many of which have ecological and evolutionary importance. (uibk.ac.at)
Taxonomically1
- This symposium will provide an overview of the bacterial, archaeal and microeukaryote diversity cataloged and taxonomically classified to date. (doe.gov)
Distinct3
- Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology. (microbial-ecology.net)
- Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order Methanosarcinales, were consistently associated with methane seep marine sediments. (mblwhoilibrary.org)
- S1 Fig), which appears to be common to all members of this bacterium on fly healthspan were due to their ability to stimulate distinct receptors for bacterial PGNs. (thehazeltines.com)
Predominance1
- Concurrent surveys of bacterial rDNAs revealed a predominance of delta -proteobacteria, in particular, close relatives of Desulfosarcina variabilis. (mblwhoilibrary.org)
Closely related1
- The unique inserts in CRISPR show virtually no similarity even between closely related bacterial strains which suggests their rapid turnover, on evolutionary scale. (biomedcentral.com)
Phyla1
- Most bacteria have not been characterised, and only about half of the bacterial phyla have species that can be grown in the laboratory. (alchetron.com)
Sulfur1
- Metagenomic analyses generated multiple populations associated with dominant ASVs, and showed characteristic traits of each lineage for sulfur, nitrogen and hydrogen metabolism. (bvsalud.org)
Species1
- The pleiotropic nature of specific gut bacterial species grows in the striatum. (thehazeltines.com)
Sequences1
- No, they were approximately the same proportion of bacterial/archaeal sequences there, but on this size fraction we noticed the bacterial/archaeal dynamics were unexpectedly rapid. (nature.com)
Environments2
- Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. (bestitservice.be)
- We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities. (biomedcentral.com)
Viral1
- For this particular study, we processed the samples by filtering several liters of water for size-fractionated DNA samples, collecting for dissolved nutrients, measuring phytoplankton biomass, and preparing microscopy slides for bacterial and viral total counts. (nature.com)
Sequence2
- However, tailed bacterial dsDNA viruses (Caudovirales), which dominate sequence and culture collections, are not representative of the environmental diversity of viruses. (elsevierpure.com)
- The pBB phylotype is a lineage within the Aquificales and, based on 16S rRNA sequence, is different enough from the members of the Aquificales to constitute a different genus. (montana.edu)
Bacteria1
- Biomarker analyses of the same sediments showed bacterial fatty acids with strong 13C depletion that are likely products of these sulfate-reducing bacteria. (mblwhoilibrary.org)
Phylum1
- Discovery of a new short alkane-metabolising archaeal phylum. (edu.au)
Dynamics1
- As for the science, our goal was to examine the dynamics of the bacterial and archaeal communities during spring-to-summer as well as their top-down and bottom-up controls, including protists and viruses. (nature.com)
Structures1
- The effect of enormous physico-chemical differences on bacterial and archaeal distributions and population structures is little understood. (bvsalud.org)
Biogeochemical1
- In situ hybridization with bacterial-specific and Aquificales -specific fluorescent oligonucleotide probes indicated the bacterial population dominated the community and most likely contributed significantly to biogeochemical cycling within the community. (montana.edu)
Organisms1
- Until about a decade ago, the general presumption was that the essential features of eukaryotic organization evolved autogenously in a proto-eukaryotic lineage, without contributions from other organisms. (asmblog.org)
Marine2
- The exploration of deep marine sediments has unearthed many new lineages of microbes. (uibk.ac.at)
- Calibrated ages obtained from the marine planktonic archaeal biomarker crenarchaeol compared favorably with varve-count ages. (mblwhoilibrary.org)
Diverse1
- However, certain lineages characterized diverse hot springs. (bvsalud.org)
Represents1
- The fictional LECA creature represents the final stage of a transition between a bacterial-archaeal prokaryote (the smallest and simplest organism) and a one-celled eukaryote (a cell with a nucleus and other organelles). (icr.org)
Communities1
- we first focused on the free-living bacterial and archaeal communities via 16S and noted, as expected, Roseobacteria and Flavobacteria associated with the bloom conditions. (nature.com)
Unknown1
- The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. (microbial-ecology.net)
Individual2
- CONCLUSIONS: High variation in community composition and estimated bacterial density among individual fish combined with low variation in community composition temporally suggests that initial community assembly involved environmental selection and random sampling/neutral effects. (bvsalud.org)
- Later during his postdoctoral work at the Massachusetts Institute of Technology he developed a high throughput approach for isolating individual bacterial cells and amplifying their genetic material, thus bypassing the need to culture these microbes in the lab. (doe.gov)
Specific1
- The same conclusion could be drawn for a more general archaeal biomarker (GDGT-0), although this biomarker proved to be less reliable due to its less-specific origin. (mblwhoilibrary.org)
Common1
- The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year, mostly in sub-Saharan Africa . (alchetron.com)
Cells2
- There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water . (alchetron.com)
- There are approximately ten times as many bacterial cells in the human microbiota as there are human cells in the body, with their largest number being in the gut flora, and a large number on the skin . (alchetron.com)
Life2
Similar1
- Biochemical studies with the Dictyoglomus native enzyme showed that this enzyme possesses some properties that are similar to other bacterial PPᵢ-PFKs. (waikato.ac.nz)