Phenotypic and Genomic Properties of Chitinispirillum Alkaliphilum Gen
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Anaerobic Digestion of the Microalga Spirulina at Extreme Alkaline Conditions: Biogas Production, Metagenome, and Metatranscriptome
ORIGINAL RESEARCH published: 22 June 2015 doi: 10.3389/fmicb.2015.00597 Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome Vímac Nolla-Ardèvol 1*, Marc Strous 1, 2, 3 and Halina E. Tegetmeyer 1, 3, 4 1 Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld, Bielefeld, Germany, 2 Department of Geoscience, University of Calgary, Calgary, AB, Canada, 3 Microbial Fitness Group, Max Planck Institute for Marine Microbiology, Bremen, Germany, 4 HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany A haloalkaline anaerobic microbial community obtained from soda lake sediments was Edited by: Mark Alexander Lever, used to inoculate anaerobic reactors for the production of methane rich biogas. The ETH Zürich, Switzerland microalga Spirulina was successfully digested by the haloalkaline microbial consortium + Reviewed by: at alkaline conditions (pH 10, 2.0 M Na ). Continuous biogas production was observed Aharon Oren, and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted The Hebrew University of Jerusalem, Israel as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S Ronald Oremland, in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g United States Geological Survey, USA Spirulina L−1 day−1 organic loading rate (OLR) were identified as the optimal operational *Correspondence: Vímac Nolla-Ardèvol, parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis Institute for Genome Research and of the supplied substrate was mainly carried out by Bacteroidetes of the “ML635J-40 Systems Biology, Center for aquatic group” while the hydrogenotrophic pathway was the main producer of methane Biotechnology, University of Bielefeld, Office G2-152, Universitätstraße 27, in a methanogenic community dominated by Methanocalculus. -
EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
Cryo-Electron Microscopy of an Extremely Halophilic Microbe: Technical Aspects
Extremophiles DOI 10.1007/s00792-016-0912-0 ORIGINAL PAPER Cryo-electron microscopy of an extremely halophilic microbe: technical aspects Daniel Bollschweiler1,2 · Miroslava Schaffer1 · C. Martin Lawrence1,3 · Harald Engelhardt1 Received: 23 November 2016 / Accepted: 19 December 2016 © The Author(s) 2016. This article is published with open access at Springerlink.com Abstract Most halophilic Archaea of the class Halobac- Keywords Halobacterium salinarum · Haloarchaea · Gas teriaceae depend on the presence of several molar sodium vesicles · Cryo-electron tomography · Focused-ion-beam chloride for growth and cell integrity. This poses problems micromachining · Vitrification for structural studies, particularly for electron microscopy, where the high salt concentration results in diminished con- trast. Since cryo-electron microscopy of intact cells pro- Introduction vides new insights into the cellular and molecular organiza- tion under close-to-live conditions, we evaluated strategies Cryo-electron microscopy and cryo-electron tomography and conditions to make halophilic microbes available for are successful techniques to investigate the structure and investigations in situ. Halobacterium salinarum, the test molecular organization of eukaryotic cells, intact bacteria, organism for this study, usually grows at 4.3 M NaCl. and archaea at close-to-live conditions (Baumeister 2015; Adaptation to lower concentrations and subsequent NaCl Plitzko 2009). The availability of direct electron detectors reduction via dialysis led to still vital cells at 3 M salt. A and a new type of phase plate for transmission electron comprehensive evaluation of vitrification parameters, thin- microscopes improve the resolution and visibility of struc- ning of frozen cells by focused-ion-beam micromachining, tural details considerably (McMullan et al. -
Department of Microbiology
SRINIVASAN COLLEGE OF ARTS & SCIENCE (Affiliated to Bharathidasan University, Trichy) PERAMBALUR – 621 212. DEPARTMENT OF MICROBIOLOGY Course : M.Sc Year: I Semester: II Course Material on: MICROBIAL PHYSIOLOGY Sub. Code : P16MB21 Prepared by : Ms. R.KIRUTHIGA, M.Sc., M.Phil., PGDHT ASSISTANT PROFESSOR / MB Month & Year : APRIL – 2020 MICROBIAL PHYSIOLOGY Unit I Cell structure and function Bacterial cell wall - Biosynthesis of peptidoglycan - outer membrane, teichoic acid – Exopolysaccharides; cytoplasmic membrane, pili, fimbriae, S-layer. Transport mechanisms – active, passive, facilitated diffusions – uni, sym, antiports. Electron carriers – artificial electron donors – inhibitors – uncouplers – energy bond – phosphorylation. Unit II Microbial growth Bacterial growth - Phases of growth curve – measurement of growth – calculations of growth rate – generation time – synchronous growth – induction of synchronous growth, synchrony index – factors affecting growth – pH, temperature, substrate and osmotic condition. Survival at extreme environments – starvation – adaptative mechanisms in thermophilic, alkalophilic, osmophilic and psychrophilic. Unit III Microbial pigments and photosynthesis Autotrophs - cyanobacteria - photosynthetic bacteria and green algae – heterotrophs – bacteria, fungi, myxotrophs. Brief account of photosynthetic and accessory pigments – chlorophyll – fluorescence, phosphorescence - bacteriochlorophyll – rhodopsin – carotenoids – phycobiliproteins. Unit IV Carbon assimilation Carbohydrates – anabolism – autotrophy – -
Acetohalobium Arabaticum Type Strain (Z-7288T)
Standards in Genomic Sciences (2010) 3:57-65 DOI:10.4056/sigs.1062906 Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288T) Johannes Sikorski1, Alla Lapidus2, Olga Chertkov3, Susan Lucas2, Alex Copeland2, Tijana Glavina Del Rio2, Matt Nolan2, Hope Tice2, Jan-Fang Cheng2, Cliff Han2,3, Evelyne Brambilla1, Sam Pitluck2, Konstantinos Liolios2, Natalia Ivanova2, Konstantinos Mavromatis2, Natalia Mikhailova2, Amrita Pati2, David Bruce2,3, Chris Detter3, Roxanne Tapia3, Lynne Goodwin2,3, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Manfred Rohde6, Markus Göker1, Stefan Spring1, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2, Nikos C. Kyrpides2, and Hans-Peter Klenk1* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: anaerobe, mesophile, halophile, chemolithotroph, methylotroph, organotroph, degradation of betaine, consumption of trimethylamine, homoacetogen, Clostridia, Halanae- robiales, GEBA Acetohalobium arabaticum Zhilina and Zavarzin 1990 is of special interest because of its physiology and its participation in the anaerobic C1-trophic chain in hypersaline environ- ments. This is the first completed genome sequence of the family Halobacteroidaceae and only the second genome sequence in the order Halanaerobiales. -
Microbiology of Oilfield Gy Ecosystems
Microbiology of oilfield ecosystems Bernard Ollivier IRD Marseille, France Oil well gggeological section Gaz Oil Water Characteristics of oil reservoirs • « Closed » ecosystems • Depth (up to 4000 m; up to several hundreth bars) • Temperature in situ : 30 to 180 °C • Water Salinities : 0 up to saturation (34% salt) ¾Importance of anaerobic microorganisms in oilfield waters 1 μm The best samplings are ¾Cores, but precautions need to be taken when drillinggpg or sampling ¾Oil waters should be collected from oilwell heads where nothing has been already injected. Kindl y provid e d by M. Mago t Studying the anaerobes Anaerobiosis : Methods -Medium pppreparation using a N2 flux. -Hunggqate’s technique -The anaerobic glove box Physico-chemical limitations to the development of microflora in oil reservoirs in situ oil biodegradation in situ oil biodegradation has never been observed in oil reservoirs where temperature is over 82°C Microbial populations in oil reservoirs 250 200 150 100 50 0 0 20 40 60 80 100 120 Tempp()erature (C) Figure kindly provided by M. Magot in situ oil biodegradation Thermophilic to hyperthermophilic Bacteria or Archaea ??? have participated to oil biodegradation Combination of high temperature and high salinity are drastic for microbial life underneath Electron acceptors available in oil field ecosystems 4 H2 + CO2 ---> CH4 + 2 H2O Methanobacterium Methanococcus CO2 + 4 H2 + 2 CO2 ---> Acetate + H + 2 H2O Acetanaerobium 4H4 H2 +H+ H2SO4 --->H> H2S+4HS + 4 H2O DlfiDesulfacinum Desulfotomaculum 2 SO4 - VFA + x H2SO4 --> y H2S + z H2O Desulfotomaculum Archaeoglobus Electron acceptors available in oil field ecosystems ?? 2- - 4H2 + S2O3 --> 2H2S + H2O + 2OH Thermotoga Desulfotomaculum Archaeoglobus 2- S2O3 Oxydation of organic matter Thermoanaerobacter coupldled to red ucti on of fhi thiosulf ate Thermo toga Electron acceptors available in oil field ecosystems ?? - Shllfhewanella putrefaciens Fe3+ - Deferribacter thermophilus - Thermotoga spp. -
Phenotypic and Genomic Properties of Chitinispirillum Alkaliphilum Gen
fmicb-07-00407 March 30, 2016 Time: 11:12 # 1 ORIGINAL RESEARCH published: 31 March 2016 doi: 10.3389/fmicb.2016.00407 Phenotypic and Genomic Properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., A Haloalkaliphilic Anaerobic Chitinolytic Bacterium Representing a Novel Class in the Phylum Fibrobacteres Dimitry Y. Sorokin1,2, Andrey L. Rakitin3, Vadim M. Gumerov3†, Alexey V. Beletsky3, Jaap S. Sinninghe Damsté4,5, Andrey V. Mardanov3 and Nikolai V. Ravin3* 1 Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Edited by: Russia, 2 Department of Biotechnology, Delft University of Technology, Delft, Netherlands, 3 Institute of Bioengineering, Andreas Teske, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia, 4 Department of Marine Organic University of North Carolina at Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and and Utrecht University, Utrecht, Netherlands, Chapel Hill, USA 5 Geochemistry, Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands Reviewed by: Antonio Ventosa, Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun University of Sevilla, Spain Takuro Nunoura, (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, Japan Agency for Marine-Earth strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium Science and Technology, Japan carbonate-based medium at pH 8.5–10.5 and total NaC concentrations from 0.4 to *Correspondence: 1.75 M. The isolate had a Gram-negative cell wall and formed lipid cysts in old cultures. Nikolai V. Ravin [email protected]; The chitinolytic activity was associated with cells. -
Metabolic Capability of a Predominant Halanaerobium Sp. in Hydraulically Fractured Gas Wells and Its Implication in Pipeline Corrosion
fmicb-07-00988 June 22, 2016 Time: 11:27 # 1 ORIGINAL RESEARCH published: 22 June 2016 doi: 10.3389/fmicb.2016.00988 Metabolic Capability of a Predominant Halanaerobium sp. in Hydraulically Fractured Gas Wells and Its Implication in Pipeline Corrosion Renxing Liang, Irene A. Davidova, Christopher R. Marks, Blake W. Stamps, Brian H. Harriman, Bradley S. Stevenson, Kathleen E. Duncan and Joseph M. Suflita* Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma, Norman, OK, USA Microbial activity associated with produced water from hydraulic fracturing operations can lead to gas souring and corrosion of carbon-steel equipment. We examined the microbial ecology of produced water and the prospective role of the prevalent Edited by: microorganisms in corrosion in a gas production field in the Barnett Shale. The John Joseph Kilbane, Illinois Institute of Technology microbial community was mainly composed of halophilic, sulfidogenic bacteria within and Intertek Westport Technology the order Halanaerobiales, which reflected the geochemical conditions of highly saline Center, USA 2− 2− − water containing sulfur species (S2O3 , SO4 , and HS ). A predominant, halophilic Reviewed by: John Stolz, bacterium (strain DL-01) was subsequently isolated and identified as belonging to the Duquesne University, USA genus Halanaerobium. The isolate could degrade guar gum, a polysaccharide polymer Romy Chakraborty, used in fracture fluids, to produce acetate and sulfide in a 10% NaCl medium at 37◦C Lawrence Berkeley National Laboratory, USA when thiosulfate was available. To mitigate potential deleterious effects of sulfide and *Correspondence: acetate, a quaternary ammonium compound was found to be an efficient biocide in Joseph M. -
WO 2016/086209 Al June 2016 (02.06.2016) W P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/086209 Al June 2016 (02.06.2016) W P O P C T (51) International Patent Classification: (74) Agents: MELLO, Jill, Ann et al; Mccarter & English, A61K 35/74 (2015.01) A61P 1/00 (2006.01) LLP, 265 Franklin Street, Boston, MA 021 10 (US). A61K 35/741 (2015.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US20 15/062809 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) International Filing Date: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 25 November 2015 (25.1 1.2015) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (26) Publication Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (30) Priority Data: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/084,536 25 November 2014 (25. 11.2014) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 62/084,537 25 November 2014 (25. 11.2014) US (84) Designated States (unless otherwise indicated, for every 62/084,540 25 November 2014 (25. -
Supplementary Information: Microbial Diversity and Methanogenic Activity of Antrim Shale Formation Waters from Recently Fracture
Supplementary information: Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells. Cornelia Wuchter 1*, Erin Banning 1◊, Tracy Mincer 1, Nicholas J. Drenzek 2† and Marco J.L. Coolen 1 1Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry Department, Woods Hole, MA 02543, USA. 2Schlumberger Doll Research, Reservoir Geosciences Department, Cambridge, MA 02139, USA. †Now at Statoil Research Center, Unconventional Shale Oil and Gas Sector, 5020-Bergen, Norway. ◊Now at Algenol Biofuels Inc., Bonita Springs, FL 34135, USA Materials and methods Bacterial and archaeal taxonomy based on capillary sequenced DGGE bands. DNA from the initial well water and incubation experiments were extracted according to (Wuchter , et al. , 2004). Partial bacterial and archaeal 16S rDNA genes were amplified by polymerase chain reaction (PCR) using a Realplex quantitative PCR system (Eppendorf, Hauppauge, NY) and reagents (with the exception of primers) as described previously (Coolen , et al. , 2009). Bacterial 16S rDNA (V4-region) was amplified with the general primers Bac341f (Muyzer , et al. , 1993) and Bac806r (Takai & Horikoshi, 2000). Archaeal 16S rDNA was first amplified with the archaea-specific primers Arch 21F (DeLong, 1992) and Arch915r (Stahl & Amann, 1991), followed by a nested PCR with the universal primer 519f (complementary 1 reverse sequence of Parch 519r (Ovreas , et al. , 1997)) and the archaeal primer Arch915r (i.e., V4-region) to increase specificity. We used the SYBR ®Green-based qPCR protocol after Coolen et al ., (2009) except for the primer annealing step, which was set to 61 °C and 40 sec for both the bacterial and archaeal primer combinations. -
Host Adaptation in Gut Firmicutes Is Associated with Sporulation Loss and Altered Transmission Cycle Hilary P
Browne et al. Genome Biology (2021) 22:204 https://doi.org/10.1186/s13059-021-02428-6 RESEARCH Open Access Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle Hilary P. Browne1*, Alexandre Almeida2,3, Nitin Kumar1, Kevin Vervier1, Anne T. Adoum2, Elisa Viciani1, Nicholas J. R. Dawson1, Samuel C. Forster1,4,5, Claire Cormie2, David Goulding2 and Trevor D. Lawley1* * Correspondence: [email protected]. uk; [email protected] Abstract 1Host-Microbiota Interactions Laboratory, Wellcome Sanger Background: Human-to-human transmission of symbiotic, anaerobic bacteria is a Institute, Hinxton, UK fundamental evolutionary adaptation essential for membership of the human gut Full list of author information is microbiota. However, despite its importance, the genomic and biological adaptations available at the end of the article underpinning symbiont transmission remain poorly understood. The Firmicutes are a dominant phylum within the intestinal microbiota that are capable of producing resistant endospores that maintain viability within the environment and germinate within the intestine to facilitate transmission. However, the impact of host transmission on the evolutionary and adaptive processes within the intestinal microbiota remains unknown. Results: We analyze 1358 genomes of Firmicutes bacteria derived from host and environment-associated habitats. Characterization of genomes as spore-forming based on the presence of sporulation-predictive genes reveals multiple losses of sporulation in many distinct lineages. Loss of sporulation in gut Firmicutes is associated with features of host-adaptation such as genome reduction and specialized metabolic capabilities. Consistent with these data, analysis of 9966 gut metagenomes from adults around the world demonstrates that bacteria now incapable of sporulation are more abundant within individuals but less prevalent in the human population compared to spore-forming bacteria.