31,466 results match your criteria Archaea Vancouver B.C.[Journal]


Origin and diversification of the cardiolipin biosynthetic pathway in the Eukarya domain.

Biochem Soc Trans 2020 Jun 3. Epub 2020 Jun 3.

Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.

Cardiolipin (CL) and its precursor phosphatidylglycerol (PG) are important anionic phospholipids widely distributed throughout all domains of life. They have key roles in several cellular processes by shaping membranes and modulating the activity of the proteins inserted into those membranes. They are synthesized by two main pathways, the so-called eukaryotic pathway, exclusively found in mitochondria, and the prokaryotic pathway, present in most bacteria and archaea. Read More

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http://dx.doi.org/10.1042/BST20190967DOI Listing

Functional and structural insights into the MRX/MRN complex, a key player in recognition and repair of DNA double-strand breaks.

Comput Struct Biotechnol J 2020 16;18:1137-1152. Epub 2020 May 16.

Dipartimento di Biotecnologie and Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy.

Chromosomal DNA double-strand breaks (DSBs) are potentially lethal DNA lesions that pose a significant threat to genome stability and therefore need to be repaired to preserve genome integrity. Eukaryotic cells possess two main mechanisms for repairing DSBs: non-homologous end-joining (NHEJ) and homologous recombination (HR). HR requires that the 5' terminated strands at both DNA ends are nucleolytically degraded by a concerted action of nucleases in a process termed DNA-end resection. Read More

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http://dx.doi.org/10.1016/j.csbj.2020.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7260605PMC

Description of CRISPR/Cas9 development and its prospect in hepatocellular carcinoma treatment.

J Exp Clin Cancer Res 2020 Jun 1;39(1):97. Epub 2020 Jun 1.

Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China.

Hepatocellular carcinoma (HCC) is one of the most common malignancies today. Patients suffer from HCC since its high malignancy and limited treatment means. With the development of genetic research, new therapeutic strategy comes up in the way of gene editing. Read More

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http://dx.doi.org/10.1186/s13046-020-01603-0DOI Listing

The Cell Membrane of spp.-Homeoviscous Adaption and Biotechnological Applications.

Int J Mol Sci 2020 May 30;21(11). Epub 2020 May 30.

Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, 1060 Vienna, Austria.

The microbial cell membrane is affected by physicochemical parameters, such as temperature and pH, but also by the specific growth rate of the host organism. Homeoviscous adaption describes the process of maintaining membrane fluidity and permeability throughout these environmental changes. Archaea, and thereby, spp. Read More

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http://dx.doi.org/10.3390/ijms21113935DOI Listing

Host Species Determines the Composition of the Prokaryotic Microbiota in Sandflies.

Pathogens 2020 May 29;9(6). Epub 2020 May 29.

Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece.

Phlebotomine sandflies are vectors of the humans' and mammals' parasite spp. Although the role of gut microbiome in the biological cycle of insects is acknowledged, we still know little about the factors modulating the composition of the gut microbiota of sandflies. We tested whether host species impose a strong structural effect on the gut microbiota of spp. Read More

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http://dx.doi.org/10.3390/pathogens9060428DOI Listing

Novel Intact Polar and Core Lipid Compositions in the Model Species, and , Reveal the Largest Lipid Diversity Amongst Thermococcales.

Biomolecules 2020 May 29;10(6). Epub 2020 May 29.

University Lyon, INSA Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.

Elucidating the lipidome of Archaea is essential to understand their tolerance to extreme environmental conditions. Previous characterizations of the lipid composition of species, a model genus of hyperthermophilic archaea belonging to the Thermococcales order, led to conflicting results, which hindered the comprehension of their membrane structure and the putative adaptive role of their lipids. In an effort to clarify the lipid composition data of the genus, we thoroughly investigated the distribution of both the core lipids (CL) and intact polar lipids (IPL) of the model and, for the first time, of , the sole obligate piezophilic hyperthermophilic archaeon known to date. Read More

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http://dx.doi.org/10.3390/biom10060830DOI Listing

Properties of the halophyte microbiome and their implications for plant salt tolerance.

Funct Plant Biol 2013 Aug;40(9):940-951

Leibniz-Institute of Vegetable- and Ornamental Crops Grossbeeren/Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany.

Saline habitats cover a wide area of our planet and halophytes (plants growing naturally in saline soils) are increasingly used for human benefits. Beside their genetic and physiological adaptations to salt, complex ecological processes affect the salinity tolerance of halophytes. Hence, prokaryotes and fungi inhabiting roots and leaves can contribute significantly to plant performance. Read More

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http://dx.doi.org/10.1071/FP12355DOI Listing

Genetic Control of Oxidative Mutagenesis in .

J Bacteriol 2020 Jun 1. Epub 2020 Jun 1.

Department of Biological Sciences, 614 Rieveschl Hall, ML0006, University of Cincinnati 513-556-9748

To identify DNA-oxidation defenses of hyperthermophilic archaea, we deleted genes encoding the putative 7,8-dihydro-8-oxoguanine (oxoG)-targeted N-glycosylase of (; Saci_01367), the Y-family DNA polymerase (; Saci_0554), or both, and measured the effects on cellular survival, replication accuracy, and oxoG bypass Spontaneous G:C to T:A transversions were elevated in all Δ and Δ constructs, and the Δ Δ double mutant lost viability at a faster rate than isogenic WT and strains. The distribution of G:C to T:A transversions within mutation-detector genes suggested that reactivity of G toward oxidation and the effect on translation contribute heavily to the pattern of mutations that are recovered. An impact of the Ogg protein on overall efficiency of bypassing oxoG in transforming DNA was evident only in the absence of Dbh, and Ogg status did not affect the accuracy of bypass. Read More

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http://dx.doi.org/10.1128/JB.00756-19DOI Listing

In-House Standard Method for Molecular Characterization of Dissolved Organic Matter by FT-ICR Mass Spectrometry.

ACS Omega 2020 May 14;5(20):11730-11736. Epub 2020 May 14.

State Key Laboratory of Heavy Oil Processing, Petroleum Molecular Engineering Center (PMEC), China University of Petroleum, Beijing 102249, China.

Electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been widely used for molecular characterization of dissolved organic matter (DOM). However, ESI FT-ICR MS generally has poor repeatability and reproducibility because of its inherent ionization mechanism and structural characteristics, which severely hindered its application in quantitative analysis of complex mixtures. In this article, we developed an in-house standard method for molecular characterization of DOM by ESI FT-ICR MS. Read More

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http://dx.doi.org/10.1021/acsomega.0c01055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7254807PMC

The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter.

Front Microbiol 2020 15;11:871. Epub 2020 May 15.

Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.

Soil microbial biomass can reach its annual maximum pool size beneath the winter snowpack and is known to decline abruptly following snowmelt in seasonally snow-covered ecosystems. Observed differences in winter versus summer microbial taxonomic composition also suggests that phylogenetically conserved traits may permit winter- versus summer-adapted microorganisms to occupy distinct niches. In this study, we sought to identify archaea, bacteria, and fungi that are associated with the soil microbial bloom overwinter and the subsequent biomass collapse following snowmelt at a high-altitude watershed in central Colorado, United States. Read More

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http://dx.doi.org/10.3389/fmicb.2020.00871DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242569PMC

[Effects of exogenous arsenic stress on bacterial and archaeal communities in two types of soils].

Ying Yong Sheng Tai Xue Bao 2020 Feb;31(2):615-624

Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, Ministry of Agriculture, Beijing 100081, China.

Mining, smelting and other activities result in arsenic accumulation in soils, with adverse impacts on the quality and safety of agricultural products and soil microorganisms. We monitored the changes of available arsenic content with incubation time after the addition of exogenous arsenic to the yellow soil (YS) and soil derived from purple sandy shale (RS). The community changes of bacteria and archaea in soils without spiked arsenic and soils after 1, 30 and 360 days of exogenous arsenic stress were measured by MiSeq high-throughput sequencing, to investigate the community adaptative mechanism of bacteria and archaea in soil under arsenic stress. Read More

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http://dx.doi.org/10.13287/j.1001-9332.202002.031DOI Listing
February 2020

Reconstitution of the human tRNA splicing endonuclease complex: insight into the regulation of pre-tRNA cleavage.

Nucleic Acids Res 2020 Jun 1. Epub 2020 Jun 1.

Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.

The splicing of tRNA introns is a critical step in pre-tRNA maturation. In archaea and eukaryotes, tRNA intron removal is catalyzed by the tRNA splicing endonuclease (TSEN) complex. Eukaryotic TSEN is comprised of four core subunits (TSEN54, TSEN2, TSEN34 and TSEN15). Read More

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http://dx.doi.org/10.1093/nar/gkaa438DOI Listing

A decade of research on the second messenger c-di-AMP.

FEMS Microbiol Rev 2020 May 30. Epub 2020 May 30.

State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China.

C-di-AMP is an emerging second messenger in bacteria and archaea that is synthesized from two molecules of ATP by diadenylate cyclases and degraded to pApA or two AMP molecules by c-di-AMP-specific phosphodiesterases. Through binding to specific protein- and riboswitch-type receptors, c-di-AMP regulates a wide variety of prokaryotic physiological functions, including maintaining the osmotic pressure, balancing central metabolism, monitoring DNA damage, and control of biofilm formation and sporulation. It mediates bacterial adaptation to a variety of environmental parameters and can also induce an immune response in host animal cells. Read More

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http://dx.doi.org/10.1093/femsre/fuaa019DOI Listing

dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes.

Sci Data 2020 May 29;7(1):164. Epub 2020 May 29.

Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.

In prokaryotes, protein phosphorylation plays a critical role in regulating a broad spectrum of biological processes and occurs mainly on various amino acids, including serine (S), threonine (T), tyrosine (Y), arginine (R), aspartic acid (D), histidine (H) and cysteine (C) residues of protein substrates. Through literature curation and public database integration, here we reported an updated database of phosphorylation sites (p-sites) in prokaryotes (dbPSP 2.0) that contains 19,296 experimentally identified p-sites in 8,586 proteins from 200 prokaryotic organisms, which belong to 12 phyla of two kingdoms, bacteria and archaea. Read More

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http://dx.doi.org/10.1038/s41597-020-0506-7DOI Listing

Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes.

Toxins (Basel) 2020 May 26;12(6). Epub 2020 May 26.

UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto de Abrigo s/n, CP 97355, Sisal, Yucatán, Mexico.

Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. Read More

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http://dx.doi.org/10.3390/toxins12060349DOI Listing

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages.

FEMS Microbiol Ecol 2020 May 28. Epub 2020 May 28.

Université Clermont Auvergne, CNRS, IRD, OPGC, Laboratoire Magmas et Volcans, F-63000 Clermont-Ferrand, France.

Basaltic rocks play a significant role in CO2 sequestration from the atmosphere during their weathering. Moreover, the primary microorganisms that colonize them, by providing mineral elements and nutrients, are shown to promote growth of diverse heterotrophic communities and plants, therefore positively impacting Earth's long-term climate balance. However, the first steps of microbial colonization and subsequent rock weathering remain poorly understood, especially regarding microbial communities over a chronological sequence. Read More

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http://dx.doi.org/10.1093/femsec/fiaa104DOI Listing

The human genetic determinism of life-threatening infectious diseases: genetic heterogeneity and physiological homogeneity?

Hum Genet 2020 May 27. Epub 2020 May 27.

St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.

Multicellular eukaryotes emerged late in evolution from an ocean of viruses, bacteria, archaea, and unicellular eukaryotes. These macroorganisms are exposed to and infected by a tremendous diversity of microorganisms. Those that are large enough can even be infected by multicellular fungi and parasites. Read More

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http://dx.doi.org/10.1007/s00439-020-02184-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7251220PMC

Impacts of Cu and Zn on the performance, microbial community dynamics and resistance genes variations during mesophilic and thermophilic anaerobic digestion of swine manure.

Bioresour Technol 2020 May 18;312:123554. Epub 2020 May 18.

State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China. Electronic address:

In this work, fate of antibiotic resistance genes (ARGs), heavy metal resistance genes (MRGs) and intI1 were investigated during mesophilic (mAD) and thermophilic anaerobic digestion (tAD) of swine manure with presence of Cu and Zn. Results showed that metal reduced the lag phase time. Cu showed stronger inhibition than Zn on archaea community and metals inhibited the growth of acetoclastic methanogens during mAD. Read More

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http://dx.doi.org/10.1016/j.biortech.2020.123554DOI Listing

The hyperthermophilic partners Nanoarchaeum and Ignicoccus stabilize their tRNA T-loops via different but structurally equivalent modifications.

Nucleic Acids Res 2020 May 27. Epub 2020 May 27.

Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.

The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis grow physically coupled under identical hyperthermic conditions. We report here two fundamentally different routes by which these archaea modify the key conserved nucleotide U54 within their tRNA T-loops. Read More

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http://dx.doi.org/10.1093/nar/gkaa411DOI Listing

The Role of Microbiomes in Pregnant Women and Offspring: Research Progress of Recent Years.

Front Pharmacol 2020 8;11:643. Epub 2020 May 8.

Department of Pharmacy, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.

Pregnancy is a complicated and delicate process, the maternal body undergoes changes on hormones, immunity, and metabolism during pregnancy to support fetal development. Microbiomes in the human body mainly live in the intestine, and the human gut microbiomes are complex, which composed of more than 500 to 1500 different bacteria, archaea, fungi, and viruses. Studies have shown that these microbiomes are not only involved in the digestion and absorption of food but also indispensable in regulating host health. Read More

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http://dx.doi.org/10.3389/fphar.2020.00643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7225329PMC

Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Biogas Upgrading Systems under Different Conditions of Temperature, pH and CO.

Microorganisms 2020 May 21;8(5). Epub 2020 May 21.

The Yangtze River Water Environment Key Laboratory of the Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.

In this study, hydrogenotrophic methanogenic mixed cultures taken from 13 lab-scale biogas upgrading systems under different temperature (20-70 °C), pH (6.0-8.5), and CO (0-10%, /) variables were systematically investigated. Read More

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http://dx.doi.org/10.3390/microorganisms8050772DOI Listing

Attributes of Physical Activity and Gut Microbiome in Adults: A Systematic Review.

Int J Sports Med 2020 May 26. Epub 2020 May 26.

The Cheryl Spencer Institute of Nursing Research, University of Haifa, Haifa, Israel.

Growing evidence shows the contribution of physical activity interventions to the gut microbiome. However, specific physical activity characteristics that can modify the gut microbiome are unknown. This review's aim was to explore the contribution of physical activity intervention characteristics on human gut microbiome composition, in terms of diversity, specific bacterial groups, and associated gut microbiome metabolites. Read More

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http://dx.doi.org/10.1055/a-1157-9257DOI Listing

Phosphorylation of the acyl-CoA binding pocket of the FadR transcription regulator in Sulfolobus acidocaldarius.

Biochimie 2020 May 23. Epub 2020 May 23.

Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium. Electronic address:

The archaeal model organism Sulfolobus acidocaldarius possesses a TetR-like transcription factor that represses a 30-kb gene cluster encoding fatty acid metabolism enzymes. Interaction of this regulator, FadR, with acyl-CoA molecules causes a DNA dissociation, which may lead to a derepression of the gene cluster. Previously, a phosphoproteome analysis revealed the phosphorylation of three consecutive amino acids in the acyl-CoA ligand binding pocket. Read More

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http://dx.doi.org/10.1016/j.biochi.2020.05.007DOI Listing

Specificities and functional coordination between the two Cas6 maturation endonucleases in sp. PCC 7120 assign orphan CRISPR arrays to three groups.

RNA Biol 2020 May 26. Epub 2020 May 26.

University of Freiburg, Faculty of Biology, Institute of Biology III , Schänzlestr. 1, D-79104, Germany.

Many bacteria and archaea possess an RNA-guided adaptive and inheritable immune system that consists of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. In most CRISPR-Cas systems, the maturation of CRISPR-derived small RNAs (crRNAs) is essential for functionality. Cas6 endonucleases function as the most frequent CRISPR RNA maturation enzymes. Read More

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http://dx.doi.org/10.1080/15476286.2020.1774197DOI Listing

Characterization of dye-linked d-amino acid dehydrogenase from Sulfurisphaera tokodaii expressed using an archaeal recombinant protein expression system.

J Biosci Bioeng 2020 May 22. Epub 2020 May 22.

Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Life Science Innovation Center, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan.

A gene encoding a dye-linked d-amino acid dehydrogenase (Dye-DADH) homologue was found in a hyperthermophilic archaeon, Sulfurisphaera tokodaii. The predicted amino acid sequence suggested that the gene product is a membrane-bound type enzyme. The gene was overexpressed in Escherichia coli, but the recombinant protein was exclusively produced as an inclusion body. Read More

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http://dx.doi.org/10.1016/j.jbiosc.2020.04.008DOI Listing

Comprehensive analysis of the pre-ribosomal RNA maturation pathway in a methanoarchaeon exposes the conserved circularization and linearization mode in archaea.

RNA Biol 2020 May 23. Epub 2020 May 23.

State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , No.1 Beichen West Road, Chaoyang District, Beijing 100101, PR China.

The ribosomal RNA (rRNA) genes are generally organized as an operon and cotranscribed into a polycistronic precursor; therefore, processing and maturation of pre-rRNAs are essential for ribosome biogenesis. However, rRNA maturation pathways of archaea, particularly of methanoarchaea, are scarcely known. Here, we thoroughly elucidated the maturation pathway of the rRNA operon (16S-tRNA-23S-tRNA-5S) in , one representative of methanoarchaea. Read More

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http://dx.doi.org/10.1080/15476286.2020.1771946DOI Listing

Discovery of 20 novel ribosomal leader candidates in bacteria and archaea.

BMC Microbiol 2020 May 24;20(1):130. Epub 2020 May 24.

Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany.

Background: RNAs perform many functions in addition to supplying coding templates, such as binding proteins. RNA-protein interactions are important in multiple processes in all domains of life, and the discovery of additional protein-binding RNAs expands the scope for studying such interactions. To find such RNAs, we exploited a form of ribosomal regulation. Read More

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http://dx.doi.org/10.1186/s12866-020-01823-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7247131PMC

Precipitation of hydrogen peroxide during winter storms and summer typhoons.

Sci Total Environ 2020 May 12;733:139377. Epub 2020 May 12.

Division of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea. Electronic address:

Hydrogen peroxide (HO) affects the activity of microbes, including archaea, and thereby influences the biogeochemical cycles of critical elements in marine and terrestrial environments. In this study, we measured the levels of HO associated with three classes of extreme wet precipitation events: winter storms, tropical storms, and typhoons. In conjunction with precipitation data, the measured HO concentration in a seawater reservoir receiving precipitation was used to estimate rainwater HO concentration and flux. Read More

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http://dx.doi.org/10.1016/j.scitotenv.2020.139377DOI Listing

Critical evidence for direct interspecies electron transfer with tungsten-based accelerants: An experimental and theoretical investigation.

Bioresour Technol 2020 May 11;311:123519. Epub 2020 May 11.

Functional Materials Laboratory (FML), School of Materials Science and Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, China.

Accelerants can significantly enhance the biodegradability in anaerobic digestion (AD), which can be attributed to the direct interspecies electron transfer (DIET) mechanism. However, critical evidence for DIET mechanism is absent. In this work, nano-scale tungsten (W)-based compounds (WC, WN, and WO) are employed to clarify the roles of W-based accelerants in AD systems. Read More

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http://dx.doi.org/10.1016/j.biortech.2020.123519DOI Listing

Temperature decouples ammonia and nitrite oxidation in greenhouse vegetable soils.

Sci Total Environ 2020 May 20;733:139391. Epub 2020 May 20.

Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China. Electronic address:

The influence of temperature on soil ammonia (NH) and nitrite (NO) oxidation and related NO accumulation in soils remain unclear. The soil potential NH oxidation (PAO) and NO oxidation (PNO) rates were evaluated over a temperature gradient of 5-45 °C in six greenhouse vegetable soils using inhibitors. The values of temperature sensitivity traits such as temperature minimum (T), temperature optimum (T), and maximum absolute temperature sensitivity (T) were also fitted to the square root growth (SQRT) and macromolecular rate theory (MMRT) models. Read More

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http://dx.doi.org/10.1016/j.scitotenv.2020.139391DOI Listing

Differential colonization of microbial communities inhabiting Lede stone in the urban and rural environment.

Sci Total Environ 2020 May 12;733:139339. Epub 2020 May 12.

Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium. Electronic address:

Air pollution is one of the main actors of stone deterioration. It influences not only the material itself but also prokaryotes colonizing rocks. Prokaryotes can affect rock substrates and biological colonization will most likely become relatively more important during the course of the 21st century. Read More

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http://dx.doi.org/10.1016/j.scitotenv.2020.139339DOI Listing

A stable simultaneous anammox, denitrifying anaerobic methane oxidation and denitrification process in integrated vertical constructed wetlands for slightly polluted wastewater.

Environ Pollut 2020 Jul 16;262:114363. Epub 2020 Mar 16.

State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. Electronic address:

Anaerobic ammonium oxidation (anammox), denitrifying anaerobic methane oxidation bacteria (DAMO) have received great attention for their excellent performance in nitrogen removal. However, not much study focused on the co-existence of anammox, DAMO, and denitrification in constructed wetlands, not to mention the advantage of their application in mitigating the necessary byproduct nitrous oxide (NO), methane (CH) from the biodegradation process. In this study, the result indicated the construction of integrated vertical constructed wetlands (IVCWs) contributed to the high-efficient stable simultaneous anammox, DAMO and denitrification (SADD) process for the nutrients removal, with denitrification being the least contributor to nitrogen reduction. Read More

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http://dx.doi.org/10.1016/j.envpol.2020.114363DOI Listing

A mixed consortium of methanotrophic archaea and bacteria boosts methane-dependent selenate reduction.

Sci Total Environ 2020 May 11;732:139310. Epub 2020 May 11.

MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China. Electronic address:

Though methane-based selenate reduction has been reported, neither the selenate load nor the removal rate could satisfy practical applications, thus limiting this technique to bio-remediate selenate pollution. In the present study, using a membrane biofilm batch reactor (MBBR), we successfully enriched a consortium performing methane-dependent selenate reduction, with enhanced reduction rates from 16.1 to 28. Read More

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http://dx.doi.org/10.1016/j.scitotenv.2020.139310DOI Listing

Prototypic SNARE Proteins Are Encoded in the Genomes of Heimdallarchaeota, Potentially Bridging the Gap between the Prokaryotes and Eukaryotes.

Curr Biol 2020 May 14. Epub 2020 May 14.

Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, Génopode, 1015 Lausanne, Switzerland. Electronic address:

A defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Read More

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http://dx.doi.org/10.1016/j.cub.2020.04.060DOI Listing

Gut Microbiota and Disorders of the Central Nervous System.

Neuroscientist 2020 May 22:1073858420918826. Epub 2020 May 22.

Experimental Neuroscience, Santa Lucia Foundation IRCCS -Rome, Italy.

The gut microbiota, consisting of bacteria, fungi, archaea, viruses, and protozoa, together with their collective genomes (microbiome), plays a key role in immune system development and maturation, gut morphology, and in performing essential metabolic functions. Several factors, including lifestyle, body mass index, diet, antibiotic use, and the environment, influence the balance of the intestinal microbiota, whose alterations (the so-called dysbiosis) in recent years have been associated with the onset and/or progression of neurological and neuropsychiatric disorders. The purpose of this narrative review is to provide an overview of the possible involvement of the microbiota-gut-brain axis in the pathogenesis of diseases of the central nervous system, with a special focus on key issues and common misjudgments on the potential contribution of specific microorganisms. Read More

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http://dx.doi.org/10.1177/1073858420918826DOI Listing

Effects of reducing chemical fertilizer combined with organic amendments on ammonia-oxidizing bacteria and archaea communities in a low-fertility red paddy field.

Environ Sci Pollut Res Int 2020 May 21. Epub 2020 May 21.

College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, People's Republic of China.

Ammonia oxidation process in soil has a great contribution to the emission of nitrous oxide, which is a hot issue in the study of N cycle of rice field ecosystem. Organic amendments which partially substitute chemical nitrogen fertilizer are widely adopted to optimizing N management and reduce the use of chemical nitrogen fertilizers in the paddy ecosystem, but their long-term effects on ammonia-oxidizing archaea (AOA) and bacteria (AOB) were not well understood. Thus, based on a 6-year field trial that comprised four fertilization strategies (CF, chemical fertilizer; PM, pig manure substituting for 20% chemical N; BF, biogas slurry substituting for 20% chemical N; and GM, milk vetch substituting for 20% chemical N) and no N fertilizer application as CK, the abundance and community structure of ammonia oxidizers were examined by using qPCR and Illumina Miseq sequencing approaches based on the functional marker genes (amoA) in a low-fertility paddy field. Read More

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http://dx.doi.org/10.1007/s11356-020-09120-5DOI Listing

16S rRNA Gene Diversity in the Salt Crust of Salar de Uyuni, Bolivia, the World's Largest Salt Flat.

Microbiol Resour Announc 2020 May 21;9(21). Epub 2020 May 21.

Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA

Salar de Uyuni is a vast, high-altitude salt flat in Bolivia with extreme physico-geochemical properties approaching multiple limits of life. Evidence for diverse halophilic bacteria and archaea was found in its surface and near-surface salt crust using 16S amplicon analysis, providing a snapshot of prokaryotic life. Read More

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http://dx.doi.org/10.1128/MRA.00374-20DOI Listing

Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, .

Microorganisms 2020 May 19;8(5). Epub 2020 May 19.

School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK.

The archaeon is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. Read More

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http://dx.doi.org/10.3390/microorganisms8050759DOI Listing

Microbial N-cycling gene abundance is affected by cover crop specie and development stage in an integrated cropping system.

Arch Microbiol 2020 May 20. Epub 2020 May 20.

Department of Crop Science, School of Agricultural Sciences, São Paulo State University, Av. Universitária 3780, Botucatu, SP, 18610-034, Brazil.

Grasses of the Urochloa genus have been widely used in crop-livestock integration systems or as cover crops in no-till systems such as in rotation with maize. Some species of Urochloa have mechanisms to reduce nitrification. However, the responses of microbial functions in crop-rotation systems with grasses and its consequence on soil N dynamics are not well-understood. Read More

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http://dx.doi.org/10.1007/s00203-020-01910-2DOI Listing

Simultaneous Removal of Dissolved Methane and Nitrogen from Synthetic Mainstream Anaerobic Effluent.

Environ Sci Technol 2020 May 28. Epub 2020 May 28.

Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia.

Anaerobic technologies have been proposed as a promising solution to enhance bioenergy recovery and to transform a wastewater treatment plant (WWTP) from an energy consumer to an energy exporter. However, 20-60% of the methane produced remains dissolved in the anaerobically treated effluent, which is a potent greenhouse gas and is easily stripped out in the aeration tank. This study aims to develop a solution using dissolved methane to support denitrification, thus simultaneously enhancing nitrogen removal and achieving beneficial use of dissolved methane. Read More

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http://dx.doi.org/10.1021/acs.est.0c00912DOI Listing
May 2020
5.330 Impact Factor

Persistent Legionnaires' Disease and Associated Antibiotic Treatment Engender a Highly Disturbed Pulmonary Microbiome Enriched in Opportunistic Microorganisms.

mBio 2020 May 19;11(3). Epub 2020 May 19.

Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France

Despite the importance of pneumonia to public health, little is known about the composition of the lung microbiome during infectious diseases, such as pneumonia, and how it evolves during antibiotic therapy. To study the possible relation of the pulmonary microbiome to the severity and outcome of this respiratory disease, we analyzed the dynamics of the pathogen and the human lung microbiome during persistent infections caused by the bacterium and their evolution during antimicrobial treatment. We collected 10 bronchoalveolar lavage fluid samples from three patients during long-term hospitalization due to pneumonia and performed a unique longitudinal study of the interkingdom microbiome, analyzing the samples for presence of bacteria, archaea, fungi, and protozoa by high-throughput Illumina sequencing of marker genes. Read More

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http://dx.doi.org/10.1128/mBio.00889-20DOI Listing

Coevolution of Eukaryote-like Vps4 and ESCRT-III Subunits in the Asgard Archaea.

mBio 2020 May 19;11(3). Epub 2020 May 19.

Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China

The emergence of the endomembrane system is a key step in the evolution of cellular complexity during eukaryogenesis. The endosomal sorting complex required for transport (ESCRT) machinery is essential and required for the endomembrane system functions in eukaryotic cells. Recently, genes encoding eukaryote-like ESCRT protein components have been identified in the genomes of Asgard archaea, a newly proposed archaeal superphylum that is thought to include the closest extant prokaryotic relatives of eukaryotes. Read More

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http://dx.doi.org/10.1128/mBio.00417-20DOI Listing

Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F-0 in Mycobacteria.

mSystems 2020 May 19;5(3). Epub 2020 May 19.

School of Biological Sciences, Monash University, Clayton, VIC, Australia

F is a low-potential redox cofactor used by diverse bacteria and archaea. In mycobacteria, this cofactor has multiple roles, including adaptation to redox stress, cell wall biosynthesis, and activation of the clinical antitubercular prodrugs pretomanid and delamanid. A recent biochemical study proposed a revised biosynthesis pathway for F in mycobacteria; it was suggested that phosphoenolpyruvate served as a metabolic precursor for this pathway, rather than 2-phospholactate as long proposed, but these findings were subsequently challenged. Read More

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http://dx.doi.org/10.1128/mSystems.00389-20DOI Listing

A Rapid, Sensitive, Low-Cost Assay for Detecting Hydrogenotrophic Methanogens in Anaerobic Digesters Using Loop-Mediated Isothermal Amplification.

Microorganisms 2020 May 15;8(5). Epub 2020 May 15.

Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.

Understanding how the presence, absence, and abundance of different microbial genera supply specific metabolic functions for anaerobic digestion (AD) and how these impact on gas production is critical for a long-term understanding and optimization of the AD process. The strictly anaerobic methanogenic archaea are essential for methane production within AD microbial communities. Methanogens are a phylogenetically diverse group that can be classified into three metabolically distinct lineages based on the substrates they use to produce methane. Read More

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http://dx.doi.org/10.3390/microorganisms8050740DOI Listing

The Archaeal Roots of the Eukaryotic Dynamic Actin Cytoskeleton.

Curr Biol 2020 May;30(10):R521-R526

Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands. Electronic address:

It is generally well accepted that eukaryotes evolved from the symbiosis of an archaeal host cell and an alphaproteobacterium, a union that ultimately gave rise to the complex, eukaryotic cells we see today. However, the catalyst of this merger, the exact nature of the cellular biology of either partner, or how this event spawned the vast majority of complex life on Earth remains enigmatic. In recent years, the discovery of the Asgard archaea, the closest known prokaryotic relatives of eukaryotes, has been monumental for addressing these unanswered questions. Read More

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http://dx.doi.org/10.1016/j.cub.2020.02.074DOI Listing

How energy flow shapes cell evolution.

Authors:
Nick Lane

Curr Biol 2020 May;30(10):R471-R476

Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. Electronic address:

How mitochondria shaped the evolution of eukaryotic complexity has been controversial for decades. The discovery of the Asgard archaea, which harbor close phylogenetic ties to the eukaryotes, supports the idea that a critical endosymbiosis between an archaeal host and a bacterial endosymbiont transformed the selective constraints present at the origin of eukaryotes. Cultured Asgard archaea are typically prokaryotic in both size and internal morphology, albeit featuring extensive protrusions. Read More

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http://dx.doi.org/10.1016/j.cub.2020.03.055DOI Listing

Author Correction: Diversity, ecology and evolution of Archaea.

Nat Microbiol 2020 May 19. Epub 2020 May 19.

Microbiology Department, University of Tennessee, Knoxville, TN, USA.

An amendment to this paper has been published and can be accessed via a link at the top of the paper. Read More

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http://dx.doi.org/10.1038/s41564-020-0741-xDOI Listing

Robust DNA protocols for tropical soils.

Heliyon 2020 May 13;6(5):e03830. Epub 2020 May 13.

Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil.

Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Read More

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http://dx.doi.org/10.1016/j.heliyon.2020.e03830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7226647PMC

Carbon recycling efficiency and phosphate turnover by marine nitrifying archaea.

Sci Adv 2020 May 8;6(19):eaba1799. Epub 2020 May 8.

MARUM Center for Marine Environmental Sciences and Dept. of Geosciences, University of Bremen, Bremen, Germany.

Thaumarchaeotal nitrifiers are among the most abundant organisms in the ocean, but still unknown is the carbon (C) yield from nitrification and the coupling of these fluxes to phosphorus (P) turnover and release of metabolites from the cell. Using a dual radiotracer approach, we found that fixed roughly 0.3 mol C, assimilated 2 mmol P, and released ca. Read More

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http://dx.doi.org/10.1126/sciadv.aba1799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7209981PMC

Emerging views of genome organization in Archaea.

J Cell Sci 2020 May 18;133(10). Epub 2020 May 18.

Biology Department, Indiana University, Bloomington, USA

Over the past decade, advances in methodologies for the determination of chromosome conformation have provided remarkable insight into the local and higher-order organization of bacterial and eukaryotic chromosomes. Locally folded domains are found in both bacterial and eukaryotic genomes, although they vary in size. Importantly, genomes of metazoans also possess higher-order organization into A- and B-type compartments, regions of transcriptionally active and inactive chromatin, respectively. Read More

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http://dx.doi.org/10.1242/jcs.243782DOI Listing