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https://www.readbyqxmd.com/read/28214513/molecular-dynamics-simulation-study-of-the-effect-of-glycerol-dialkyl-glycerol-tetraether-hydroxylation-on-membrane-thermostability
#1
Carme Huguet, Susanne Fietz, Antoni Rosell-Melé, Xavier Daura, Lionel Costenaro
Archaeal tetraether membrane lipids span the whole membrane width and present two C40 isoprenoid chains bound by two glycerol groups (or one glycerol and calditol). These lipids confer stability and maintain the membrane fluidity in mesophile to extremophile environments, making them very attractive for biotechnological applications. The isoprenoid lipid composition in archaeal membranes varies with temperature, which has placed these lipids in the focus of paleo-climatological studies for about a decade. Non-hydroxylated isoprenoid archaeal lipids are typically used as paleo-thermometry proxies, but recently identified hydroxylated (OH) derivatives have also been proposed as temperature proxies...
February 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28213705/responses-of-soil-methanogens-methanotrophs-and-methane-fluxes-to-land-use-conversion-and-fertilization-in-a-hilly-red-soil-region-of-southern-china
#2
Huifeng Liu, Xing Wu, Zongshan Li, Qing Wang, Dan Liu, Guohua Liu
Changes in land-uses and fertilization are important factors regulating methane (CH4) emissions from paddy soils. However, the responses of soil CH4 emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH4 fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH4 fluxes were quantified by static chamber and gas chromatography technology...
February 17, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28213542/plant-community-and-nitrogen-deposition-as-drivers-of-%C3%AE-and-%C3%AE-prokaryotic-diversity-in-reconstructed-oil-sands-soils-and-natural-boreal-forest-soils
#3
Jacynthe Masse, Cindy E Prescott, Sébastien Renaut, Yves Terrat, Sue J Grayston
The Athabasca Oil Sands deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess if soil prokaryotic α- and β-diversity in oil-sands soils reconstructed 20-30 years previously, and planted to one of three vegetation types (coniferous or deciduous trees and grassland) were similar to those found in natural boreal-forest soils subject to wildfire disturbance...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28211189/influence-of-oxygen-availability-on-the-activities-of-ammonia-oxidizing-archaea
#4
Wei Qin, Kelley A Meinhardt, James W Moffett, Allan H Devol, E Virginia Armbrust, Anitra E Ingalls, David A Stahl
Recent studies point to the importance of oxygen (O2 ) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O2 tension in oceanic oxygen minimum zones (OMZs), and O2 availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N2 O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low μM O2 concentrations, characteristic of suboxic regions of OMZs (<10 µM O2 ), and that atmospheric concentrations of O2 may inhibit the growth of some environmental populations...
February 17, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28210633/potential-usefulness-of-streptococcus-pneumoniae-extracellular-membrane-vesicles-as-antibacterial-vaccines
#5
Chi-Won Choi, Edmond Changkyun Park, Sung Ho Yun, Sang-Yeop Lee, Seung Il Kim, Gun-Hwa Kim
The secretion of extracellular membrane vesicles (EMVs) is a common phenomenon that occurs in archaea, bacteria, and mammalian cells. The EMVs of bacteria play important roles in their virulence, biogenesis mechanisms, and host cell interactions. Bacterial EMVs have recently become the focus of attention because of their potential as highly effective vaccines that cause few side effects. Here, we isolated the EMVs of Streptococcus pneumoniae and examined their potential as new vaccine candidates. Although the S...
2017: Journal of Immunology Research
https://www.readbyqxmd.com/read/28206708/physiological-metabolic-and-biotechnological-features-of-extremely-thermophilic-microorganisms
#6
REVIEW
James A Counts, Benjamin M Zeldes, Laura L Lee, Christopher T Straub, Michael W W Adams, Robert M Kelly
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water...
February 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28204908/a-large-scale-evaluation-of-algorithms-to-calculate-average-nucleotide-identity
#7
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun
Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Calculating ANI usually involves the fragmentation of genome sequences, followed by nucleotide sequence search, alignment, and identity calculation. The original algorithm to calculate ANI used the BLAST program as its search engine. An improved ANI algorithm, called OrthoANI, was developed to accommodate the concept of orthology. Here, we compared four algorithms to compute ANI, namely ANIb (ANI algorithm using BLAST), ANIm (ANI using MUMmer), OrthoANIb (OrthoANI using BLAST) and OrthoANIu (OrthoANI using USEARCH) using >100,000 pairs of genomes with various genome sizes...
February 15, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28202757/the-viral-gene-orf79-encodes-a-repressor-regulating-induction-of-the-lytic-life-cycle-in-the-haloalkaliphilic-virus-%C3%AF-ch1
#8
Regina Selb, Christian Derntl, Reinhard Klein, Beatrix Alte, Christoph Hofbauer, Martin Kaufmann, Judith Beraha, Léa Schöner, Angela Witte
In this study, we describe the construction of the first genetically modified mutant of a halovirus infecting haloalkaliphilic Archaea By random choice we targeted ORF79, a so far uncharacterized viral gene of the haloalkaliphilic virus φCh1. We used a PEG-mediated transformation method to deliver a disruption cassette into a lysogenic strain of the haloalkaliphilic archaeon Natrialba magadii bearing φCh1 as provirus. This approach yielded mutant virus particles carrying a disrupted version of the ORF79. Disruption of ORF79 did not influence morphology of the mature virions...
February 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28202591/non-classical-phase-diagram-for-virus-bacterial-coevolution-mediated-by-clustered-regularly-interspaced-short-palindromic-repeats
#9
Pu Han, Michael W Deem
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202392/sophisticated-regulation-of-transcriptional-factors-by-the-bacterial-phosphoenolpyruvate-sugar-phosphotransferase-system
#10
REVIEW
Anne Galinier, Josef Deutscher
The phosphoenolpyruvate:sugar phosphotransferase system (PTS) is a carbohydrate transport and phosphorylation system present in bacteria of all different phyla and in archaea. It is usually composed of three proteins or protein complexes, enzyme I, HPr and enzyme II, which are phosphorylated at histidine or cysteine residues. However, in many bacteria, HPr can also be phosphorylated at a serine residue. The PTS functions not only as carbohydrate transporter, but also regulates numerous cellular processes by either phosphorylating its target proteins or by interacting with them in a phosphorylation-dependent manner...
February 12, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28198664/microbial-fouling-and-corrosion-of-carbon-steel-in-deep-anoxic-alkaline-groundwater
#11
Pauliina Rajala, Malin Bomberg, Mikko Vepsäläinen, Leena Carpén
Understanding the corrosion of carbon steel materials of low and intermediate level radioactive waste under repository conditions is crucial to ensure the safe storage of radioactive contaminated materials. The waste will be in contact with the concrete of repository silos and storage containers, and eventually with groundwater. In this study, the corrosion of carbon steel under repository conditions as well as the microbial community forming biofilm on the carbon steel samples, consisting of bacteria, archaea, and fungi, was studied over a period of three years in a groundwater environment with and without inserted concrete...
February 2017: Biofouling
https://www.readbyqxmd.com/read/28197855/soil-microbial-community-responses-to-contamination-with-silver-aluminium-oxide-and-silicon-dioxide-nanoparticles
#12
C F McGee, S Storey, N Clipson, E Doyle
Soil microorganisms are key contributors to nutrient cycling and are essential for the maintenance of healthy soils and sustainable agriculture. Although the antimicrobial effects of a broad range of nanoparticulate substances have been characterised in vitro, little is known about the impact of these compounds on microbial communities in environments such as soil. In this study, the effect of three widely used nanoparticulates (silver, silicon dioxide and aluminium oxide) on bacterial and fungal communities in an agricultural pastureland soil was examined in a microcosm-based experiment using a combination of enzyme analysis, molecular fingerprinting and amplicon sequencing...
February 14, 2017: Ecotoxicology
https://www.readbyqxmd.com/read/28197141/metabolomic-and-metagenomic-analysis-of-two-crude-oil-production-pipelines-experiencing-differential-rates-of-corrosion
#13
Vincent Bonifay, Boris Wawrik, Jan Sunner, Emily C Snodgrass, Egemen Aydin, Kathleen E Duncan, Amy V Callaghan, Athenia Oldham, Turid Liengen, Iwona Beech
Corrosion processes in two North Sea oil production pipelines were studied by analyzing pig envelope samples via metagenomic and metabolomic techniques. Both production systems have similar physico-chemical properties and injection waters are treated with nitrate, but one pipeline experiences severe corrosion and the other does not. Early and late pigging material was collected to gain insight into the potential causes for differential corrosion rates. Metabolites were extracted and analyzed via ultra-high performance liquid chromatography/high-resolution mass spectrometry with electrospray ionization (ESI) in both positive and negative ion modes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28196981/rna-based-recognition-and-targeting-sowing-the-seeds-of-specificity
#14
REVIEW
Stanislaw A Gorski, Jörg Vogel, Jennifer A Doudna
RNA is involved in the regulation of multiple cellular processes, often by forming sequence-specific base pairs with cellular RNA or DNA targets that must be identified among the large number of nucleic acids in a cell. Several RNA-based regulatory systems in eukaryotes, bacteria and archaea, including microRNAs (miRNAs), small interfering RNAs (siRNAs), CRISPR RNAs (crRNAs) and small RNAs (sRNAs) that are dependent on the RNA chaperone protein Hfq, achieve specificity using similar strategies. Central to their function is the presentation of short 'seed sequences' within a ribonucleoprotein complex to facilitate the search for and recognition of targets...
February 15, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28195581/cultivation-and-characterization-of-candidatus-nitrosocosmicus-exaquare-an-ammonia-oxidizing-archaeon-from-a-municipal-wastewater-treatment-system
#15
Laura A Sauder, Mads Albertsen, Katja Engel, Jasmin Schwarz, Per H Nielsen, Michael Wagner, Josh D Neufeld
Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca...
February 14, 2017: ISME Journal
https://www.readbyqxmd.com/read/28194147/freshwater-recirculating-aquaculture-system-operations-drive-biofilter-bacterial-community-shifts-around-a-stable-nitrifying-consortium-of-ammonia-oxidizing-archaea-and-comammox-nitrospira
#16
Ryan P Bartelme, Sandra L McLellan, Ryan J Newton
Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as a byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species are thought to be the primary nitrifiers present in RAS biofilters. We explored this assertion by characterizing the biofilter bacterial and archaeal community of a commercial scale freshwater RAS that has been in operation for >15 years...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28192430/computational-identification-of-the-selenocysteine-trna-trnasec-in-genomes
#17
Didac Santesmasses, Marco Mariotti, Roderic Guigó
Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages...
February 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28191504/distinct-biogeographic-patterns-for-archaea-bacteria-and-fungi-along-the-vegetation-gradient-at-the-continental-scale-in-eastern-china
#18
Bin Ma, Zhongmin Dai, Haizhen Wang, Melissa Dsouza, Xingmei Liu, Yan He, Jianjun Wu, Jorge L M Rodrigues, Jack A Gilbert, Philip C Brookes, Jianming Xu
The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China...
January 2017: MSystems
https://www.readbyqxmd.com/read/28188879/effects-of-dietary-supplementation-of-active-dried-yeast-on-fecal-methanogenic-archaea-diversity-in-dairy-cows
#19
Dingxing Jin, Kun Kang, Hongze Wang, Zhisheng Wang, Bai Xue, Lizhi Wang, Feng Xu, Quanhui Peng
This study aimed to investigate the effects of dietary supplementation of different dosages of active dried yeast (ADY) on the fecal methanogenic archaea community of dairy cattle. Twelve multiparous, healthy, mid-lactating Holstein dairy cows (body weight: 584 ± 23.2 kg, milk produced: 26.3 ± 1.22 kg/d) were randomly assigned to one of three treatments (control, ADY2, and ADY4) according to body weight with four replicates per treatment. Cows in the control group were fed conventional rations without ADY supplementation, while cows in the ADY2 and ADY4 group were fed rations supplemented with ADY at 2 or 4 g/d/head...
February 7, 2017: Anaerobe
https://www.readbyqxmd.com/read/28186905/hmmcas-a-web-tool-for-the-identification-and-domain-annotations-of-cas-proteins
#20
Guoshi Chai, Min Yu, Lixu Jiang, Yaocong Duan, Jian Huang
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) adaptive immune systems are discovered in many bacteria and most archaea. These systems are encoded by cas (CRISPR-associated) operons that have an extremely diverse architecture. The most crucial step in the depiction of cas operons composition is the identification of cas genes or Cas proteins. With the continuous increase of the newly sequenced archaeal and bacterial genomes, the recognition of new Cas proteins is becoming possible, which not only provides candidates for novel genome editing tools but also helps to understand the prokaryotic immune system better...
February 7, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
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