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Timothy J Williams, Michelle Allen, Bernhard Tschitschko, Ricardo Cavicchioli
Haloarchaea are heterotrophic members of the Archaea that thrive in hypersaline environments, often feeding off the glycerol that is produced as an osmolyte by eucaryotic Dunaliella during primary production. In this study we analyzed glycerol metabolism genes in closed genomes of haloarchaea, and examined published data describing the growth properties of haloarchaea and experimental data for the enzymes involved. By integrating the genomic data with knowledge from the literature, we derived an understanding of the ecophysiology and evolutionary properties of glycerol catabolic pathways in haloarchaea...
October 21, 2016: Environmental Microbiology
Gokul Turaga, Stephen P Edmondson, Kelley Smith, John William Shriver
The structure of Archaeal chromatin or nucleoid is believed to have characteristics similar to that found in both eukaryotes and bacteria. Recent comparative studies have suggested that DNA compaction in Archaea requires a bridging protein (e.g. Alba) along with either a wrapping protein (e.g. a histone) or a bending protein such as Sac7d. While x-ray crystal structures demonstrate that Sac7d binds as a monomer to create a significant kink in duplex DNA, the structure of a multiprotein-DNA complex has not been established...
October 21, 2016: Biochemistry
Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau
BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer...
October 20, 2016: BMC Evolutionary Biology
Ana C Henriques, Rui M S Azevedo, Paolo De Marco
Methanesulfonic acid (MSA) is a relevant intermediate of the biogeochemical cycle of sulfur and environmental microorganisms assume an important role in the mineralization of this compound. Several methylotrophic bacterial strains able to grow on MSA have been isolated from soil or marine water and two conserved operons, msmABCD coding for MSA monooxygenase and msmEFGH coding for a transport system, have been repeatedly encountered in most of these strains. Homologous sequences have also been amplified directly from the environment or observed in marine metagenomic data, but these showed a base composition (G + C content) very different from their counterparts from cultivated bacteria...
2016: PeerJ
Janine Kamke, Sandra Kittelmann, Priya Soni, Yang Li, Michael Tavendale, Siva Ganesh, Peter H Janssen, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts...
October 19, 2016: Microbiome
Isabel M López-Lara, Otto Geiger
The glycerophospholipids phosphatidylethanolamine, phosphatidylglycerol (PG), and cardiolipin (CL) are major structural components of bacterial membranes. In some bacteria, phosphatidylcholine or phosphatidylinositol and its derivatives form part of the membrane. PG or CL can be modified with the amino acid residues lysine, alanine, or arginine. Diacylglycerol is the lipid anchor from which syntheses of phosphorus-free glycerolipids, such as glycolipids, sulfolipids, or homoserine-derived lipids initiate. Many membrane lipids are subject to turnover and some of them are recycled...
October 17, 2016: Biochimica et Biophysica Acta
Roberto Danovaro, Antonio Dell'Anno, Cinzia Corinaldesi, Eugenio Rastelli, Ricardo Cavicchioli, Mart Krupovic, Rachel T Noble, Takuro Nunoura, David Prangishvili
Viruses are the most abundant biological entities in the world's oceans, and they play a crucial role in global biogeochemical cycles. In deep-sea ecosystems, archaea and bacteria drive major nutrient cycles, and viruses are largely responsible for their mortality, thereby exerting important controls on microbial dynamics. However, the relative impact of viruses on archaea compared to bacteria is unknown, limiting our understanding of the factors controlling the functioning of marine systems at a global scale...
October 2016: Science Advances
Lorenzo Calisti, Irene Benni, Matilde Cardoso Trabuco, Paola Baiocco, Barbara Ruzicka, Alberto Boffi, Elisabetta Falvo, Francesco Malatesta, Alessandra Bonamore
BACKGROUND: A set of engineered ferritin mutants from Archaeoglobus fulgidus (Af-Ft) and Pyrococcus furiosus (Pf-Ft) bearing cysteine thiols in selected topological positions inside or outside the ferritin shell have been obtained. The two apo-proteins were taken as model systems for ferritin internal cavity accessibility in that Af-Ft is characterized by the presence of a 45Å wide aperture on the protein surface whereas Pf-Ft displays canonical (threefold) channels. METHODS: Thiol reactivity has been probed in kinetic experiments in order to assess the protein matrix permeation properties towards the bulky thiol reactive DTNB (5,5'-dithiobis-2-nitrobenzoic acid) molecule...
October 15, 2016: Biochimica et Biophysica Acta
Cornelia U Welte, Olivia Rasigraf, Annika Vaksmaa, Wouter Versantvoort, Arslan Arshad, Huub J M Op den Camp, Mike S M Jetten, Claudia Lüke, Joachim Reimann
Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens...
October 18, 2016: Environmental Microbiology Reports
Carmen Sarcinelli, Gabriella Fiorentino, Elio Pizzo, Simonetta Bartolucci, Danila Limauro
Peroxiredoxins (Prxs) are ubiquitous thiol peroxidases that are involved in the reduction of peroxides. It has been reported that prokaryotic Prxs generally show greater structural robustness than their eukaryotic counterparts, making them less prone to inactivation by overoxidation. This difference has inspired the search for new antioxidants from prokaryotic sources that can be used as possible therapeutic biodrugs. Bacterioferritin comigratory proteins (Bcps) of the hyperthermophilic archaeon Sulfolobus solfataricus that belong to the Prx family have recently been characterized...
2016: Archaea: An International Microbiological Journal
Rafael Laso-Pérez, Gunter Wegener, Katrin Knittel, Friedrich Widdel, Katie J Harding, Viola Krukenberg, Dimitri V Meier, Michael Richter, Halina E Tegetmeyer, Dietmar Riedel, Hans-Hermann Richnow, Lorenz Adrian, Thorsten Reemtsma, Oliver Lechtenfeld, Florin Musat
The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors that are believed to be all specific for C1-compounds. Here we found that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4-hydrocarbon butane. The archaea, proposed genus Candidatus Syntrophoarchaeum, showed the characteristic autofluorescence of methanogens, and contained highly expressed genes encoding enzymes similar to methyl-coenzyme M reductase (MCR)...
October 17, 2016: Nature
Jack A Gilbert
It is now well accepted that our modern lifestyle has certain implications for our health (Schaub et al., ), mainly as a result of our willingness to remove ourselves from the biological diversity of our natural environments (Roduit et al., ), while still being drawn inextricably to interact with it (Kellert and Wilson, ). Much of our interaction with the biological world is shaped by our interaction with the microbiological world. The bacteria, fungi, viruses, archaea and protists that comprise the microbiome of this planet, are also key to the development and normal functioning of our bodies...
October 17, 2016: Microbial Biotechnology
Martha M Yeshanew, Luigi Frunzo, Vincenzo Luongo, Francesco Pirozzi, Piet N L Lens, Giovanni Esposito
The present work studied the start-up process of a mesophilic (37 ± 2 °C) anaerobic fluidized bed reactor (AFBR) operated at a hydraulic retention time (HRT) of 20 days using synthetic carbohydrate rich wastewater. Anox Kaldness-K1 carriers were used as biofilm carrier material. The reactor performance and biofilm formation were evaluated during the process. The start-up process at lower liquid recirculation flow rate enhanced the biofilm formation and reactor performance. The organic substrate composition had a major impact on early colonization of methanogenic archaea onto the surface of the Kaldness carriers during the start-up process...
October 13, 2016: Journal of Environmental Management
Vanessa Tripp, Roman Martin, Alvaro Orell, Omer S Alkhnbashi, Rolf Backofen, Lennart Randau
Archaeal and eukaryotic organisms contain sets of C/D box s(no)RNAs with guide sequences that determine ribose 2'-O-methylation sites of target RNAs. The composition of these C/D box sRNA sets is highly variable between organisms and results in varying RNA modification patterns which are important for ribosomal RNA folding and stability. Little is known about the genomic organization of C/D box sRNA genes in archaea. Here, we aimed to obtain first insights into the biogenesis of these archaeal C/D box sRNAs and analyzed the genetic context of more than 300 archaeal sRNA genes...
October 14, 2016: Molecular Microbiology
Yun-Feng Duan, Xian-Wang Kong, Andreas Schramm, Rodrigo Labouriau, Jørgen Eriksen, Søren O Petersen
: Grassland cultivation can mobilize large pools of N in the soil, with a potential for N leaching and N2O emissions. Spraying with the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) before cultivation was simulated with soil columns where residue distribution corresponded to ploughing or rotovation, to study effects of soil-residue contact on N transformations. DMPP was sprayed on above-ground parts of ryegrass and white clover before incorporation. During a 42-day incubation, soil mineral N dynamics, potential ammonia oxidation (PAO) and denitrifying enzyme activity (DEA), nitrifier and denitrifier populations, and N2O emissions were investigated...
October 14, 2016: Applied and Environmental Microbiology
Xi Sun, Lusheng Zhu, Jinhua Wang, Jun Wang, Benying Su, Tong Liu, Cheng Zhang, Chong Gao, Yuting Shao
Ionic liquids (ILs) were considered as "green" solvents and have been used widely because of their excellent properties. But ILs are not as "green" as has been suggested, and the toxic effects of ILs on organisms have been shown in recent years. In the present study, the toxic effects of the IL 1-octyl-3-methylimidazolium tetrafluoroborate ([Omim]BF4) on soil enzyme activity and soil microbial communities at three different concentrations (1.0, 5.0 and 10.0mg/kg) and a control treatment over 40 days of incubation time (sampled on days 10, 20, 30 and 40) were examined under laboratory conditions...
October 11, 2016: Ecotoxicology and Environmental Safety
I-Min A Chen, Victor M Markowitz, Ken Chu, Krishna Palaniappan, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Evan Andersen, Marcel Huntemann, Neha Varghese, Michalis Hadjithomas, Kristin Tennessen, Torben Nielsen, Natalia N Ivanova, Nikos C Kyrpides
The Integrated Microbial Genomes with Microbiome Samples (IMG/M: system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives...
October 13, 2016: Nucleic Acids Research
Zhao-Wei Ding, Yong-Ze Lu, Liang Fu, Jing Ding, Raymond J Zeng
In this study, the coculture system of denitrifying anaerobic methane oxidation (DAMO) microbes and anaerobic ammonium oxidation (anammox) bacteria was successfully enriched in a hollow-fiber membrane biofilm reactor (HfMBR) using freshwater sediment as the inoculum. The maximal removal rates of nitrate and ammonium were 78 mg N/L/day (131 mg N/m(2)/day) and 26 mg N/L/day (43 mg N/m(2)/day), respectively. Due to the high rate of methane mass transfer in HfMBR, the activity of DAMO archaea continued to increase during the enrichment period, indicating that HfMBR could be a powerful tool to enrich DAMO microorganisms...
October 12, 2016: Applied Microbiology and Biotechnology
Jenna L Shelton, Denise M Akob, Jennifer C McIntosh, Noah Fierer, John R Spear, Peter D Warwick, John E McCray
Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry...
2016: Frontiers in Microbiology
M Florencia Haurat, Ana Sofia Figueiredo, Lena Hoffmann, Lingling Li, Katharina Herr, Amanda Wilson, Morgan Beeby, Jörg Schaber, Sonja-Verena Albers
Organisms have evolved motility organelles that allow them to move to favorable habitats. Cells integrate environmental stimuli into intracellular signals to motility machineries to direct this migration. Many motility organelles are complex surface appendages that have evolved a tight, hierarchical regulation of expression. In the crenearchaeon Sulfolobus acidocaldarius, biosynthesis of the archaellum is regulated by regulatory network proteins that control expression of archaellum components in a phosphorylation-dependent manner...
October 12, 2016: Molecular Microbiology
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