29,627 results match your criteria Archaea Vancouver B.C.[Journal]


Patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge in Lhasa River.

Ecotoxicol Environ Saf 2019 Apr 19;178:195-201. Epub 2019 Apr 19.

Department of Water Resources and Hydropower Engineering, Wuhan University, Wuhan, 430000, China. Electronic address:

The increased anthropogenic activities in the Tibetan Plateau may threaten the river environmental safety. However, limited information is available on the Lhasa River in the Tibetan Plateau, which is known as the remaining pure land on Earth. Here, we firstly investigated the distribution patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge along the reaches of the Lhasa River. Read More

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http://dx.doi.org/10.1016/j.ecoenv.2019.03.107DOI Listing

Abundance and diversity of nitrogen-removing microorganisms in the UASB-anammox reactor.

PLoS One 2019 22;14(4):e0215615. Epub 2019 Apr 22.

College of Resources and Environmental Science, Xinjiang University, Urumqi, China.

Anaerobic ammonium oxidation is considered to be the most economical and low-energy biological nitrogen removal process. So far, anammox bacteria have not yet been purified from cultures. Some nitrogen-removing microorganisms cooperate to perform the anammox process. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215615PLOS

Ferric citrate, nitrate, saponin, and their combinations affect in-vitro ruminal fermentation, production of sulfide and methane, and abundance of select microbial populations.

J Appl Microbiol 2019 Apr 20. Epub 2019 Apr 20.

Department of Animal Sciences, The Ohio State University, Columbus, Ohio, 43210-1094, USA.

Aims: This study investigated the effects of ferric citrate, nitrate, and saponin, both individually and in combination, on sulfidogenesis, methanogenesis, rumen fermentation, and abundances of select microbial populations using in vitro rumen cultures.

Methods And Results: Ferric citrate (50 mg L ), Quillaja saponin (0·6 g L ), and sodium nitrate (5 mmol L ) were used in in vitro ruminal fermentation. Ferric citrate alone, its combination with saponin and/or nitrate lowered the aqueous sulfide concentration and total sulfide production. Read More

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http://dx.doi.org/10.1111/jam.14286DOI Listing

Pore timing: the evolutionary origins of the nucleus and nuclear pore complex.

F1000Res 2019 3;8. Epub 2019 Apr 3.

The Rockefeller University, New York, USA.

The name "eukaryote" is derived from Greek, meaning "true kernel", and describes the domain of organisms whose cells have a nucleus. The nucleus is thus the defining feature of eukaryotes and distinguishes them from prokaryotes (Archaea and Bacteria), whose cells lack nuclei. Despite this, we discuss the intriguing possibility that organisms on the path from the first eukaryotic common ancestor to the last common ancestor of all eukaryotes did not possess a nucleus at all-at least not in a form we would recognize today-and that the nucleus in fact arrived relatively late in the evolution of eukaryotes. Read More

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http://dx.doi.org/10.12688/f1000research.16402.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449795PMC

Diurnal Temperature Variation and Plants Drive Latitudinal Patterns in Seasonal Dynamics of Soil Microbial Community.

Front Microbiol 2019 2;10:674. Epub 2019 Apr 2.

Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.

Seasonality, an exogenous driver, motivates the biological and ecological temporal dynamics of animal and plant communities. Underexplored microbial temporal endogenous dynamics hinders the prediction of microbial response to climate change. To elucidate temporal dynamics of microbial communities, temporal turnover rates, phylogenetic relatedness, and species interactions were integrated to compare those of a series of forest ecosystems along latitudinal gradients. Read More

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https://www.frontiersin.org/article/10.3389/fmicb.2019.00674
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http://dx.doi.org/10.3389/fmicb.2019.00674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454054PMC
April 2019
1 Read

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.

Nat Commun 2019 Apr 18;10(1):1816. Epub 2019 Apr 18.

Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. Read More

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http://www.nature.com/articles/s41467-019-09747-0
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http://dx.doi.org/10.1038/s41467-019-09747-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472368PMC
April 2019
1 Read

Impact of intron removal from tRNA genes on Saccharomyces cerevisiae.

Nucleic Acids Res 2019 Apr 18. Epub 2019 Apr 18.

Graduate School of Life Science, University of Hyogo, Ako-gun 678-1297, Japan.

In eukaryotes and archaea, tRNA genes frequently contain introns, which are removed during maturation. However, biological roles of tRNA introns remain elusive. Here, we constructed a complete set of Saccharomyces cerevisiae strains in which the introns were removed from all the synonymous genes encoding 10 different tRNA species. Read More

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http://dx.doi.org/10.1093/nar/gkz270DOI Listing

Identification of new members of alkaliphilic lipases in archaea and metagenome database using reconstruction of ancestral sequences.

3 Biotech 2019 May 4;9(5):165. Epub 2019 Apr 4.

1Department of Microbiology, Maharaja Ganga Singh University, 334004 Bikaner, India.

The application of bioinformatics in lipase research has the potential to discover robust members from different genomic/metagenomic databses. In this study, we explored the diversity and distribution of alkaliphilic lipases in archaea domain and metagenome data sets through phylogenetic survey. Reconstructed ancestral sequence of alkaphilic lipase was used to search the homologous alkaliphilic lipases among the archaea and metagenome public databases. Read More

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http://dx.doi.org/10.1007/s13205-019-1693-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449409PMC

Deciphering the Assembly Processes of the Key Ecological Assemblages of Microbial Communities in Thirteen Full-Scale Wastewater Treatment Plants.

Microbes Environ 2019 Apr 16. Epub 2019 Apr 16.

CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences.

Limited information is currently available on the assembly processes (deterministic vs. stochastic) shaping the compositions of key microbial communities in activated sludge (AS). The relative importance of deterministic and stochastic processes for key bacterial and archaeal assemblages (i. Read More

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http://dx.doi.org/10.1264/jsme2.ME18107DOI Listing

Polyhydroxyalkanoate Biosynthesis at the Edge of Water Activitiy-Haloarchaea as Biopolyester Factories.

Authors:
Martin Koller

Bioengineering (Basel) 2019 Apr 16;6(2). Epub 2019 Apr 16.

University of Graz, Office of Research Management and Service, c/o Institute of Chemistry, NAWI Graz, Heinrichstrasse 28/III, 8010 Graz, Austria.

Haloarchaea, the extremely halophilic branch of the Archaea domain, encompass a steadily increasing number of genera and associated species which accumulate polyhydroxyalkanoate biopolyesters in their cytoplasm. Such ancient organisms, which thrive in highly challenging, often hostile habitats characterized by salinities between 100 and 300 g/L NaCl, have the potential to outperform established polyhydroxyalkanoate production strains. As detailed in the review, this optimization presents due to multifarious reasons, including: cultivation setups at extreme salinities can be performed at minimized sterility precautions by excluding the growth of microbial contaminants; the high inner-osmotic pressure in haloarchaea cells facilitates the recovery of intracellular biopolyester granules by cell disintegration in hypo-osmotic media; many haloarchaea utilize carbon-rich waste streams as main substrates for growth and polyhydroxyalkanoate biosynthesis, which allows coupling polyhydroxyalkanoate production with bio-economic waste management; finally, in many cases, haloarchaea are reported to produce copolyesters from structurally unrelated inexpensive substrates, and polyhydroxyalkanoate biosynthesis often occurs in parallel to the production of additional marketable bio-products like pigments or polysaccharides. Read More

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http://dx.doi.org/10.3390/bioengineering6020034DOI Listing

Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters.

Microb Biotechnol 2019 Apr 17. Epub 2019 Apr 17.

Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany.

Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1111/1751-7915.13
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http://dx.doi.org/10.1111/1751-7915.13409DOI Listing
April 2019
1 Read

Physiological roles of antisense RNAs in prokaryotes.

Biochimie 2019 Apr 14. Epub 2019 Apr 14.

CNRS UMR8261, IBPC, 13 Rue Pierre et Marie Curie, 75005, Paris, France. Electronic address:

Prokaryotes encounter constant and often brutal modifications to their environment. In order to survive, they need to maintain fitness, which includes adapting their protein expression patterns. Many factors control gene expression but this review focuses on just one, namely antisense RNAs (asRNAs), a class of non-coding RNAs (ncRNAs) characterized by their location in cis and their perfect complementarity with their targets. Read More

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http://dx.doi.org/10.1016/j.biochi.2019.04.015DOI Listing

RNA stabilization in hyperthermophilic archaea.

Ann N Y Acad Sci 2019 Apr 17. Epub 2019 Apr 17.

Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Analyses of the RNA metabolism of hyperthermophilic archaea highlight the efficiency of regulatory RNAs and RNA-guided processes at extreme temperatures. These organisms must overcome the intrinsic thermolability of RNAs. Elevated levels of RNA modifications and structured GC-rich regions are observed for many universal noncoding RNA families. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1111/nyas.14060
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http://dx.doi.org/10.1111/nyas.14060DOI Listing
April 2019
1 Read

[Effects of long-term fertilization on soil microbial abundance in farmland of the Loess Plateau, China].

Ying Yong Sheng Tai Xue Bao 2019 Apr;30(4):1351-1358

Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, Shannxi, China.

Based on a long-term experiment in the Changwu Agro-ecological Experimental Station, the real-time PCR analysis was used to examine the soil microbial abundance and to reveal the effects on soil microbial community under different long-term fertilization systems. The results showed that compared to the CK (barren field), the population of bacteria increased by 21% and archaea by 32% in treatment with inorganic fertilizer application. The abundance of bacteria in the treatment of chemical fertilizer combined with organic fertilizer increased by 37% and archaea by 36%. Read More

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http://dx.doi.org/10.13287/j.1001-9332.201904.003DOI Listing
April 2019
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Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters.

Mol Ecol 2019 Apr 16. Epub 2019 Apr 16.

School of Marine Sciences, Ningbo University, Ningbo, 315211, China.

Marine archaea are crucial in biogeochemical cycles, but their horizontal spatial variability, assembly processes, and microbial associations across complex coastal waters still lack characterizations at high coverage. Using a dense sampling strategy, we investigated horizontal variability in total Archaeal, Thaumarchaeota Marine Group (MG) I, and Euryarchaeota MGII communities and associations of MGI/MGII with other microbes in surface waters with contrasting environmental characteristics across ~ 200 km by 16S rRNA gene amplicon sequencing. Total Archaeal communities were extremely dominated by MGI and/or MGII (98. Read More

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http://dx.doi.org/10.1111/mec.15105DOI Listing

Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array.

FEMS Microbiol Lett 2019 Apr 17. Epub 2019 Apr 17.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894.

Screening of genomic and metagenomic databases for new variants of CRISPR-Cas systems increasingly results in the discovery of derived variants that do not seem to possess the interference capacity and are implicated in functions distinct from adaptive immunity. We describe an extremely derived putative class 1 CRISPR-Cas system that is present in many Halobacteria and consists of distant homologs of the Cas5 and Cas7 protein along with an uncharacterized conserved protein and various nucleases. We hypothesize that, although this system lacks typical CRISPR effectors or a CRISPR array, it functions as a RNA-dependent defense mechanism that, unlike other derived CRISPR-Cas, utilizes alternative nucleases to cleave invader genomes. Read More

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http://dx.doi.org/10.1093/femsle/fnz079DOI Listing

The Archaellum of Methanospirillum hungatei Is Electrically Conductive.

MBio 2019 Apr 16;10(2). Epub 2019 Apr 16.

Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA

Microbially produced electrically conductive protein filaments are of interest because they can function as conduits for long-range biological electron transfer. They also show promise as sustainably produced electronic materials. Until now, microbially produced conductive protein filaments have been reported only for bacteria. Read More

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http://mbio.asm.org/lookup/doi/10.1128/mBio.00579-19
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http://dx.doi.org/10.1128/mBio.00579-19DOI Listing
April 2019
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Metabopolis: scalable network layout for biological pathway diagrams in urban map style.

BMC Bioinformatics 2019 Apr 15;20(1):187. Epub 2019 Apr 15.

Research Division of Computer Graphics, Institute of Visual Computing and Human- Centered Technology, TU Wien, Vienna, Austria.

Background: Biological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments and layout algorithms often sacrifice low-level details to maintain high-level information, which complicates the entire image to large biochemical systems such as human metabolic pathways.

Results: Our work is inspired by concepts from urban planning since we create a visual hierarchy of biological pathways, which is analogous to city blocks and grid-like road networks in an urban area. Read More

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http://dx.doi.org/10.1186/s12859-019-2779-4DOI Listing
April 2019
2 Reads

Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.

BMC Genomics 2019 Apr 16;20(1):299. Epub 2019 Apr 16.

Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.

Background: Crl, identified for curli production, is a small transcription factor that stimulates the association of the σ factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms.

Results: In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σ regulon in this bacterium. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5619-zDOI Listing
April 2019
1 Read

Fluid surface coatings for solid-state nanopores: comparison of phospholipid bilayers and archaea-Inspired lipid monolayers.

Nanotechnology 2019 Apr 16. Epub 2019 Apr 16.

Universite de Fribourg Adolphe Merkle Institute, Fribourg, SWITZERLAND.

In the context of sensing and characterizing single proteins with synthetic nanopores, lipid bilayer coatings provide at least four benefits: First, they minimize unwanted protein adhesion to the pore walls by exposing a zwitterionic, fluid surface. Second, they can slow down protein translocation and rotation by the opportunity to tether proteins with a lipid anchor to the fluid bilayer coating. Third, they provide the possibility to impart analyte specificity by including lipid anchors with a specific receptor or ligand in the coating. Read More

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http://dx.doi.org/10.1088/1361-6528/ab19e6DOI Listing
April 2019
1 Read

Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce.

Environ Microbiol 2019 Apr 16. Epub 2019 Apr 16.

Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Großbeeren, Germany.

Long-term agricultural fertilization strategies gradually change soil properties including the associated microbial communities. Cultivated crops recruit beneficial microbes from the surrounding soil environment via root exudates. In this study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.14
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http://dx.doi.org/10.1111/1462-2920.14631DOI Listing
April 2019
2 Reads

Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting.

Nat Commun 2019 Apr 15;10(1):1742. Epub 2019 Apr 15.

Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany.

Na/H antiporters exchange sodium ions and protons on opposite sides of lipid membranes. The electroneutral Na/H antiporter NhaP from archaea Pyrococcus abyssi (PaNhaP) is a functional homolog of the human Na/H exchanger NHE1, which is an important drug target. Here we resolve the Na and H transport cycle of PaNhaP by transition-path sampling. Read More

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http://dx.doi.org/10.1038/s41467-019-09739-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465308PMC
April 2019
2 Reads

Direct production of polyhydroxybutyrate from waste starch by newly-isolated Bacillus aryabhattai T34-N4.

Environ Technol 2019 Apr 16:1-30. Epub 2019 Apr 16.

a Japan International Research Center for Agricultural Sciences 1-1 , Ohwashi, Tsukuba , Ibaraki 305-8686 , Japan.

Polyhydroxybutyrate (PHB) is a natural microbial polyester produced by a variety of bacteria and archaea from renewable resources. PHB resembles some petrochemical plastics but is completely biodegradable. It is desirable to identify suitable microbial strains and develop processes that can directly use starch from agricultural wastes without commercial amylase treatment. Read More

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http://dx.doi.org/10.1080/09593330.2019.1608314DOI Listing

Characterization of Two Toxin-Antitoxin Systems in Deep-Sea sp. SCSIO 02999.

Mar Drugs 2019 Apr 4;17(4). Epub 2019 Apr 4.

Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.

Toxin-antitoxin (TA) systems are ubiquitous and abundant genetic elements in bacteria and archaea. Most previous TA studies have focused on commensal and pathogenic bacteria, but have rarely focused on marine bacteria, especially those isolated from the deep sea. Here, we identified and characterized three putative TA pairs in the deep-sea-derived sp. Read More

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http://dx.doi.org/10.3390/md17040211DOI Listing
April 2019
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Isolation and culture of Methanobrevibacter smithii by co-culture with hydrogen-producing bacteria on agar plates.

Clin Microbiol Infect 2019 Apr 12. Epub 2019 Apr 12.

Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France. Electronic address:

Objective: Methanogenic archaea are considered as extremely oxygen-sensitive organisms and their culture is fastidious, requiring specific equipment. We report here the conditions allowing the cultivation of M. smithii in an anaerobic chamber without hydrogen addition. Read More

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http://dx.doi.org/10.1016/j.cmi.2019.04.008DOI Listing

Evaluation of a robust engineered enzyme towards organophosphorus insecticide bioremediation using planarians as biosensors.

Chem Biol Interact 2019 Apr 12;306:96-103. Epub 2019 Apr 12.

Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France. Electronic address:

Organophosphorus compounds (OPs) are neurotoxic molecules developed as insecticides and chemical warfare nerve agents (CWNAs). They are covalent inhibitors of acetylcholinesterase (AChE), a key enzyme in central and peripheral nervous systems and are responsible for numerous poisonings worldwide. Many animal models have been studied over the years but finding a suitable in vivo model to account for both acute toxicity and long-term exposure remains a topical issue. Read More

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http://dx.doi.org/10.1016/j.cbi.2019.04.013DOI Listing

Candidatus Syntrophosphaera thermopropionivorans: a novel player in syntrophic propionate oxidation during anaerobic digestion.

Environ Microbiol Rep 2019 Apr 15. Epub 2019 Apr 15.

Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany.

Propionate is an important intermediate in the anaerobic mineralization of organic matter. In methanogenic environments its degradation relies on syntrophic associations between syntrophic propionate-oxidizing bacteria (SPOB) and Archaea. However, only ten isolated species have been identified as SPOB so far. Read More

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http://dx.doi.org/10.1111/1758-2229.12759DOI Listing

Properties of a cryptic lysyl oxidase from haloarchaeon .

PeerJ 2019 5;7:e6691. Epub 2019 Apr 5.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.

Background: Lysyl oxidases (LOX) have been extensively studied in mammals, whereas properties and functions of recently found homologues in prokaryotic genomes remain enigmatic.

Methods: LOX open reading frame was cloned from in an expression vector. Recombinant lysyl oxidase (HTU-LOX) proteins were purified using metal affinity chromatography under denaturing conditions followed by refolding. Read More

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https://peerj.com/articles/6691
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http://dx.doi.org/10.7717/peerj.6691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452851PMC
April 2019
2 Reads

Long-Term Encapsulated Nitrate Supplementation Modulates Rumen Microbial Diversity and Rumen Fermentation to Reduce Methane Emission in Grazing Steers.

Front Microbiol 2019 29;10:614. Epub 2019 Mar 29.

Department of Animal Science, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Universidade Estadual Paulista, Jaboticabal, Brazil.

This study investigated the long-term effects (13 months) of encapsulated nitrate supplementation (ENS) on enteric methane emissions, rumen fermentation parameters, ruminal bacteria, and diversity of archaea in grazing beef cattle. We used a total of thirty-two Nellore steers (initial BW of 197 ± 15.3 kg), 12 of which were fitted with rumen cannulas. Read More

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http://dx.doi.org/10.3389/fmicb.2019.00614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449429PMC

Haloferax sulfurifontis GUMFAZ2 producing xylanase-free cellulase retrieved from Haliclona sp. inhabiting rocky shore of Anjuna, Goa-India.

J Basic Microbiol 2019 Apr 13. Epub 2019 Apr 13.

Department of Microbiology, Goa University, Taleigao Plateau, Goa, India.

Salt stable cellulases are implicated in detritic food webs of marine invertebrates for their role in degradation of cellulosic material. A haloarchaeon, Haloferax sulfurifontis GUMFAZ2 producing cellulase was successfully isolated from marine Haliclona sp., a sponge inhabiting the rocky intertidal region of Anjuna, Goa. Read More

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http://doi.wiley.com/10.1002/jobm.201800672
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http://dx.doi.org/10.1002/jobm.201800672DOI Listing
April 2019
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Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches.

Zoology (Jena) 2019 04 1;133:81-87. Epub 2019 Mar 1.

Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. Electronic address:

Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e. Read More

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http://dx.doi.org/10.1016/j.zool.2019.02.007DOI Listing

A new type of DNA phosphorothioation-based antiviral system in archaea.

Nat Commun 2019 04 11;10(1):1688. Epub 2019 Apr 11.

Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China.

Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Read More

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http://www.nature.com/articles/s41467-019-09390-9
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http://dx.doi.org/10.1038/s41467-019-09390-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6459918PMC
April 2019
6 Reads

Specific quorum sensing molecules of ammonia oxidizers and their role during ammonium metabolism in Zhalong wetland, China.

Sci Total Environ 2019 May 19;666:1106-1113. Epub 2019 Feb 19.

State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China; School of Environment, Harbin Institute of Technology, Harbin, China. Electronic address:

The primary challenge of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) surviving in wetlands are the rapid and unpredictable environmental changes. To adapt to a fluctuant environment, ammonia oxidizers have to communicate with each other via acyl-homoserine lactones (AHLs). In this study, AOA and AOB in the soil samples taken from Zhalong wetland were incubated. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00489697193075
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http://dx.doi.org/10.1016/j.scitotenv.2019.02.261DOI Listing
May 2019
4 Reads

Why the Lipid Divide? Membrane Proteins as Drivers of the Split between the Lipids of the Three Domains of Life.

Authors:
Victor Sojo

Bioessays 2019 Apr 10:e1800251. Epub 2019 Apr 10.

College for Life Sciences, Wissenschaftskolleg zu Berlin (Institute for Advanced Study, Berlin), Germany.

Recent results from engineered and natural samples show that the starkly different lipids of archaea and bacteria can form stable hybrid membranes. But if the two types can mix, why don't they? That is, why do most bacteria and all eukaryotes have only typically bacterial lipids, and archaea archaeal lipids? It is suggested here that the reason may lie on the other main component of cellular membranes: membrane proteins, and their close adaptation to the lipids. Archaeal lipids in modern bacteria could suggest that the last universal common ancestor (LUCA) had both lipid types. Read More

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http://dx.doi.org/10.1002/bies.201800251DOI Listing
April 2019
1 Read

Effect of Benzophenone-3 on performance, structure and microbial metabolism in an EGSB system.

Environ Technol 2019 Apr 10:1-31. Epub 2019 Apr 10.

a GDCON Research Group, Faculty of Engineering, University Research Headquarters (SIU) , University of Antioquia , Street 70 # 52-21, Medellín , Colombia .

Benzophenone-3 is an organic compound widely used as a UV filter, which has been reported as water pollutant and is connected with endocrine disruption in humans and animals. Expanded granular sludge beds (EGSB) are a form of an anaerobic digestion system, which has been successfully evaluated for wastewater treatment, and the removal of different compounds, however little is known about the effect of compounds as Benzophenone-3 in the performance of EGSB systems. In this study, we evaluate the effect of BP-3 on the performance, microbial structure and metabolism of EGSB reactors. Read More

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http://dx.doi.org/10.1080/09593330.2019.1606287DOI Listing

Natural tuning of restriction endonuclease synthesis by cluster of rare arginine codons.

Sci Rep 2019 Apr 9;9(1):5808. Epub 2019 Apr 9.

Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk, 80-308, Poland.

Restriction-modification (R-M) systems are highly widespread among bacteria and archaea, and they appear to play a pivotal role in modulating horizontal gene transfer, as well as in protecting the host organism against viruses and other invasive DNA particles. Type II R-M systems specify two independent enzymes: a restriction endonuclease (REase) and protective DNA methyltransferase (MTase). If the cell is to survive, the counteracting activities as toxin and antitoxin, must be finely balanced in vivo. Read More

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http://dx.doi.org/10.1038/s41598-019-42311-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456624PMC

Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes.

MBio 2019 Apr 9;10(2). Epub 2019 Apr 9.

Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA

Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. -ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation. This review will discuss the current state of the field in bacteria and some of the work in archaea, focusing on both mechanisms of -ε-lysine acetylation and methods to identify, quantify, and characterize specific acetyllysines. Read More

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http://mbio.asm.org/lookup/doi/10.1128/mBio.02708-18
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http://dx.doi.org/10.1128/mBio.02708-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456759PMC
April 2019
1 Read

The Primary Antisense Transcriptome of NRC-1.

Genes (Basel) 2019 Apr 5;10(4). Epub 2019 Apr 5.

Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, São Paulo 14049-900, Brazil.

Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3' ends of these transcripts. Read More

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http://dx.doi.org/10.3390/genes10040280DOI Listing

Characterization of microbial community dynamics during the anaerobic co-digestion of thermally pre-treated slaughterhouse wastes with glycerin addition.

Bioprocess Biosyst Eng 2019 Apr 6. Epub 2019 Apr 6.

GIRO Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, Caldes de Montbui, 08140, Barcelona, Spain.

Microbial community dynamics during the anaerobic co-digestion of pig manure, pasteurized slaughterhouse waste and glycerin were studied in a lab-scale CSTR. The feed composition was optimized through progressive co-substrate additions for enhanced methane production and organic matter removal without accumulation of intermediate compounds. Microbial community structure of biomass samples was studied by means of qPCR and DGGE profiling of 16S rRNA genes (Bacteria and Archaea), and genus-specific qPCR of the methyl coenzyme M reductase gene (mcrA), which encodes for an enzyme universally involved in methanogenesis. Read More

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http://dx.doi.org/10.1007/s00449-019-02115-8DOI Listing
April 2019
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Tolerance of the freeze-dried mouse sperm nucleus to temperatures ranging from -196 °C to 150 °C.

Sci Rep 2019 Apr 5;9(1):5719. Epub 2019 Apr 5.

Advanced Biotechnology Center, University of Yamanashi, 4-4-37 Takeda, Kofu-shi, Yamanashi, Japan.

It has long been believed that tolerance against extreme environments is possible only for 'lower' groups, such as archaea, bacteria or tardigrades, and not for more 'advanced' species. Here, we demonstrated that the mammalian sperm nucleus also exhibited strong tolerance to cold and hot temperatures. When mouse spermatozoa were freeze-dried (FD), similar to the anhydrobiosis of Tardigrades, all spermatozoa were ostensibly dead after rehydration. Read More

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http://dx.doi.org/10.1038/s41598-019-42062-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450870PMC
April 2019
1 Read

A revised biosynthetic pathway for the cofactor F in prokaryotes.

Nat Commun 2019 04 5;10(1):1558. Epub 2019 Apr 5.

Synthetic Biology Future Science Platform, CSIRO Land and Water, Canberra, 2601, ACT, Australia.

Cofactor F plays critical roles in primary and secondary metabolism in a range of bacteria and archaea as a low-potential hydride transfer agent. It mediates a variety of important redox transformations involved in bacterial persistence, antibiotic biosynthesis, pro-drug activation and methanogenesis. However, the biosynthetic pathway for F has not been fully elucidated: neither the enzyme that generates the putative intermediate 2-phospho-L-lactate, nor the function of the FMN-binding C-terminal domain of the γ-glutamyl ligase (FbiB) in bacteria are known. Read More

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http://dx.doi.org/10.1038/s41467-019-09534-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450877PMC

Conservation of conformational dynamics across prokaryotic actins.

PLoS Comput Biol 2019 Apr 5;15(4):e1006683. Epub 2019 Apr 5.

Department of Bioengineering, Stanford University, Stanford, CA, United States of America.

The actin family of cytoskeletal proteins is essential to the physiology of virtually all archaea, bacteria, and eukaryotes. While X-ray crystallography and electron microscopy have revealed structural homologies among actin-family proteins, these techniques cannot probe molecular-scale conformational dynamics. Here, we use all-atom molecular dynamic simulations to reveal conserved dynamical behaviors in four prokaryotic actin homologs: MreB, FtsA, ParM, and crenactin. Read More

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http://dx.doi.org/10.1371/journal.pcbi.1006683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450608PMC
April 2019
2 Reads

Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes.

Authors:
Rudolf K Thauer

Biochemistry 2019 Apr 5. Epub 2019 Apr 5.

Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Strasse 10 , Marburg 35043 , Germany.

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. The active enzyme harbors the nickel(I) hydrocorphin coenzyme F-430 as a prosthetic group and catalyzes the reversible reduction of methyl-coenzyme M (CH-S-CoM) with coenzyme B (HS-CoM) to methane and CoM-S-S-CoB. MCR is also involved in anaerobic methane oxidation in reverse of methanogenesis and most probably in the anaerobic oxidation of ethane, propane, and butane. Read More

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http://pubs.acs.org/doi/10.1021/acs.biochem.9b00164
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http://dx.doi.org/10.1021/acs.biochem.9b00164DOI Listing
April 2019
7 Reads

A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.

Nat Commun 2019 04 4;10(1):1542. Epub 2019 Apr 4.

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

Fatty acid metabolism and its regulation are known to play important roles in bacteria and eukaryotes. By contrast, although certain archaea appear to metabolize fatty acids, the regulation of the underlying pathways in these organisms remains unclear. Here, we show that a TetR-family transcriptional regulator (FadR) is involved in regulation of fatty acid metabolism in the crenarchaeon Sulfolobus acidocaldarius. Read More

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http://dx.doi.org/10.1038/s41467-019-09479-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449355PMC
April 2019
2 Reads
10.742 Impact Factor

EvoMining reveals the origin and fate of natural product biosynthetic enzymes.

Microb Genom 2019 Apr 4. Epub 2019 Apr 4.

Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, México.

Natural products (NPs), or specialized metabolites, are important for medicine and agriculture alike, and for the fitness of the organisms that produce them. NP genome-mining aims at extracting biosynthetic information from the genomes of microbes presumed to produce these compounds. Typically, canonical enzyme sequences from known biosynthetic systems are identified after sequence similarity searches. Read More

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http://dx.doi.org/10.1099/mgen.0.000260DOI Listing
April 2019
1 Read

New views on an old enzyme: allosteric regulation and evolution of archaeal pyruvate kinases.

FEBS J 2019 Apr 4. Epub 2019 Apr 4.

Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany.

Pyruvate kinases (PKs) synthesize ATP as the final step of glycolysis in the three domains of life. PKs from most bacteria and eukarya are allosteric enzymes that are activated by sugar phosphates, e.g. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1111/febs.14837
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http://dx.doi.org/10.1111/febs.14837DOI Listing
April 2019
12 Reads

Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria.

Int J Syst Evol Microbiol 2019 Apr 2. Epub 2019 Apr 2.

3​Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands.

Two mesophilic, neutrophilic and aerobic marine ammonia-oxidizing archaea, designated strains NF5 and D3C, were isolated from coastal surface water of the Northern Adriatic Sea. Cells were straight small rods 0.20-0. Read More

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http://dx.doi.org/10.1099/ijsem.0.003360DOI Listing

Microbial diversity in a coastal environment with co-existing upwelling and mud-banks along the south west coast of India.

Mol Biol Rep 2019 Apr 1. Epub 2019 Apr 1.

Regional Centre, CSIR-National Institute of Oceanography, Dr. Salim Ali Road, Post Box No. 1913, Kochi, Kerala, 682 018, India.

Upwelling and mud banks are two prominent oceanographic features in the coastal waters along the south west coast of India during the southwest monsoon (MON) season. The present study investigates the microbial diversity in the coastal environments of Alappuzha, India, where upwelling and mud banks co-exist. Water samples were collected from three stations, M1, M2, and M3, on a weekly basis to estimate the physico-chemical parameters and microbial abundance (MA). Read More

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http://dx.doi.org/10.1007/s11033-019-04766-yDOI Listing

Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments.

Front Microbiol 2019 18;10:499. Epub 2019 Mar 18.

Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.

Oxygen reducing terminal oxidases differ with respect to their subunit composition, heme groups, operon structure, and affinity for O. Six families of terminal oxidases are currently recognized, all of which occur in alphaproteobacterial genomes, two of which are also present in mitochondria. Many alphaproteobacteria encode several different terminal oxidases, likely reflecting ecological versatility with respect to oxygen levels. Read More

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http://dx.doi.org/10.3389/fmicb.2019.00499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431628PMC

Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism.

Nat Microbiol 2019 Apr 1. Epub 2019 Apr 1.

Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

The origin of eukaryotes represents an unresolved puzzle in evolutionary biology. Current research suggests that eukaryotes evolved from a merger between a host of archaeal descent and an alphaproteobacterial endosymbiont. The discovery of the Asgard archaea, a proposed archaeal superphylum that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota suggested to comprise the closest archaeal relatives of eukaryotes, has helped to elucidate the identity of the putative archaeal host. Read More

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http://dx.doi.org/10.1038/s41564-019-0406-9DOI Listing