(12) Patent Application Publication (10) Pub. No.: US 2006/0234346A1 Retallack Et Al
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Hydrogenophaga Electricum Sp. Nov., Isolated from Anodic Biofilms of an Acetate-Fed Microbial Fuel Cell
J. Gen. Appl. Microbiol., 59, 261‒266 (2013) Full Paper Hydrogenophaga electricum sp. nov., isolated from anodic biofilms of an acetate-fed microbial fuel cell Zen-ichiro Kimura and Satoshi Okabe* Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060‒8628, Japan (Received October 25, 2012; Accepted April 2, 2013) A Gram-negative, non-spore-forming, rod-shaped bacterial strain, AR20T, was isolated from an- odic biofilms of an acetate-fed microbial fuel cell in Japan and subjected to a polyphasic taxo- nomic study. Strain AR20T grew optimally at pH 7.0‒8.0 and 25°C. It contained Q-8 as the pre- dominant ubiquinone and C16:0, summed feature 3 (C16:1ω7c and/or iso-C15:02OH), and C18:1ω7c as the major fatty acids. The DNA G+C content was 67.1 mol%. A neighbor-joining phylogenetic tree revealed that strain AR20T clustered with three type strains of the genus Hydrogenophaga (H. flava, H. bisanensis and H. pseudoflava). Strain AR20T exhibited 16S rRNA gene sequence similarity values of 95.8‒97.7% to the type strains of the genus Hydrogenophaga. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain AR20T is considered a novel species of the genus Hydrogenophaga, for which the name Hydrogenophaga electricum sp. nov. is pro- posed. The type strain is AR20T (= KCTC 32195T = NBRC 109341T). Key Words—Hydrogenophaga electricum; hydrogenotrophic exoelectrogen; microbial fuel cell Introduction the MFC was analyzed. Results showed that bacteria belonging to the genera Geobacter and Hydrogenoph- Microbial fuel cells (MFCs) are devices that are able aga were abundantly present in the anodic biofilm to directly convert the chemical energy of organic community (Kimura and Okabe, 2013). -
Rapport Nederlands
Moleculaire detectie van bacteriën in dekaarde Dr. J.J.P. Baars & dr. G. Straatsma Plant Research International B.V., Wageningen December 2007 Rapport nummer 2007-10 © 2007 Wageningen, Plant Research International B.V. Alle rechten voorbehouden. Niets uit deze uitgave mag worden verveelvoudigd, opgeslagen in een geautomatiseerd gegevensbestand, of openbaar gemaakt, in enige vorm of op enige wijze, hetzij elektronisch, mechanisch, door fotokopieën, opnamen of enige andere manier zonder voorafgaande schriftelijke toestemming van Plant Research International B.V. Exemplaren van dit rapport kunnen bij de (eerste) auteur worden besteld. Bij toezending wordt een factuur toegevoegd; de kosten (incl. verzend- en administratiekosten) bedragen € 50 per exemplaar. Plant Research International B.V. Adres : Droevendaalsesteeg 1, Wageningen : Postbus 16, 6700 AA Wageningen Tel. : 0317 - 47 70 00 Fax : 0317 - 41 80 94 E-mail : [email protected] Internet : www.pri.wur.nl Inhoudsopgave pagina 1. Samenvatting 1 2. Inleiding 3 3. Methodiek 8 Algemene werkwijze 8 Bestudeerde monsters 8 Monsters uit praktijkteelten 8 Monsters uit proefteelten 9 Alternatieve analyse m.b.v. DGGE 10 Vaststellen van verschillen tussen de bacterie-gemeenschappen op myceliumstrengen en in de omringende dekaarde. 11 4. Resultaten 13 Monsters uit praktijkteelten 13 Monsters uit proefteelten 16 Alternatieve analyse m.b.v. DGGE 23 Vaststellen van verschillen tussen de bacterie-gemeenschappen op myceliumstrengen en in de omringende dekaarde. 25 5. Discussie 28 6. Conclusies 33 7. Suggesties voor verder onderzoek 35 8. Gebruikte literatuur. 37 Bijlage I. Bacteriesoorten geïsoleerd uit dekaarde en van mycelium uit commerciële teelten I-1 Bijlage II. Bacteriesoorten geïsoleerd uit dekaarde en van mycelium uit experimentele teelten II-1 1 1. -
Università Degli Studi Di Padova Dipartimento Di Biomedicina Comparata Ed Alimentazione
UNIVERSITÀ DEGLI STUDI DI PADOVA DIPARTIMENTO DI BIOMEDICINA COMPARATA ED ALIMENTAZIONE SCUOLA DI DOTTORATO IN SCIENZE VETERINARIE Curriculum Unico Ciclo XXVIII PhD Thesis INTO THE BLUE: Spoilage phenotypes of Pseudomonas fluorescens in food matrices Director of the School: Illustrious Professor Gianfranco Gabai Department of Comparative Biomedicine and Food Science Supervisor: Dr Barbara Cardazzo Department of Comparative Biomedicine and Food Science PhD Student: Andreani Nadia Andrea 1061930 Academic year 2015 To my family of origin and my family that is to be To my beloved uncle Piero Science needs freedom, and freedom presupposes responsibility… (Professor Gerhard Gottschalk, Göttingen, 30th September 2015, ProkaGENOMICS Conference) Table of Contents Table of Contents Table of Contents ..................................................................................................................... VII List of Tables............................................................................................................................. XI List of Illustrations ................................................................................................................ XIII ABSTRACT .............................................................................................................................. XV ESPOSIZIONE RIASSUNTIVA ............................................................................................ XVII ACKNOWLEDGEMENTS .................................................................................................... -
Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis
Fish bacterial flora identification via rapid cellular fatty acid analysis Item Type Thesis Authors Morey, Amit Download date 09/10/2021 08:41:29 Link to Item http://hdl.handle.net/11122/4939 FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS By Amit Morey /V RECOMMENDED: $ Advisory Committe/ Chair < r Head, Interdisciplinary iProgram in Seafood Science and Nutrition /-■ x ? APPROVED: Dean, SchooLof Fisheries and Ocfcan Sciences de3n of the Graduate School Date FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Amit Morey, M.F.Sc. Fairbanks, Alaska h r A Q t ■ ^% 0 /v AlA s ((0 August 2007 ^>c0^b Abstract Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception of Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon ( Oncorhynchus gorbuscha) were determined by the rapid method. -
(12) United States Patent (10) Patent No.: US 7476,532 B2 Schneider Et Al
USOO7476532B2 (12) United States Patent (10) Patent No.: US 7476,532 B2 Schneider et al. (45) Date of Patent: Jan. 13, 2009 (54) MANNITOL INDUCED PROMOTER Makrides, S.C., "Strategies for achieving high-level expression of SYSTEMIS IN BACTERAL, HOST CELLS genes in Escherichia coli,” Microbiol. Rev. 60(3):512-538 (Sep. 1996). (75) Inventors: J. Carrie Schneider, San Diego, CA Sánchez-Romero, J., and De Lorenzo, V., "Genetic engineering of nonpathogenic Pseudomonas strains as biocatalysts for industrial (US); Bettina Rosner, San Diego, CA and environmental process.” in Manual of Industrial Microbiology (US) and Biotechnology, Demain, A, and Davies, J., eds. (ASM Press, Washington, D.C., 1999), pp. 460-474. (73) Assignee: Dow Global Technologies Inc., Schneider J.C., et al., “Auxotrophic markers pyrF and proC can Midland, MI (US) replace antibiotic markers on protein production plasmids in high cell-density Pseudomonas fluorescens fermentation.” Biotechnol. (*) Notice: Subject to any disclaimer, the term of this Prog., 21(2):343-8 (Mar.-Apr. 2005). patent is extended or adjusted under 35 Schweizer, H.P.. "Vectors to express foreign genes and techniques to U.S.C. 154(b) by 0 days. monitor gene expression in Pseudomonads. Curr: Opin. Biotechnol., 12(5):439-445 (Oct. 2001). (21) Appl. No.: 11/447,553 Slater, R., and Williams, R. “The expression of foreign DNA in bacteria.” in Molecular Biology and Biotechnology, Walker, J., and (22) Filed: Jun. 6, 2006 Rapley, R., eds. (The Royal Society of Chemistry, Cambridge, UK, 2000), pp. 125-154. (65) Prior Publication Data Stevens, R.C., “Design of high-throughput methods of protein pro duction for structural biology.” Structure, 8(9):R177-R185 (Sep. -
Phenotypic and Genetic Diversity of Pseudomonads
PHENOTYPIC AND GENETIC DIVERSITY OF PSEUDOMONADS ASSOCIATED WITH THE ROOTS OF FIELD-GROWN CANOLA A Thesis Submitted to the College of Graduate Studies and Research In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon By Danielle Lynn Marie Hirkala © Copyright Danielle Lynn Marie Hirkala, November 2006. All rights reserved. PERMISSION TO USE In presenting this thesis in partial fulfilment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon, Saskatchewan, S7N 5A8 i ABSTRACT Pseudomonads, particularly the fluorescent pseudomonads, are common rhizosphere bacteria accounting for a significant portion of the culturable rhizosphere bacteria. -
Isolation and Morphological Characterization of Novel Bacterial
BIOLOGIA (PAKISTAN) PKISSN 0006 – 3096 (Print) June, 2018, 64 (1), 119-128 ISSN 2313 – 206X (On-Line) Isolation and morphological characterization of novel bacterial Endophytes from Citrus and evaluation for antifungal potential against Alternaria solani SEHRISH MUSHTAQ1, MUHAMMAD SHAFIQ1, MUHAMMAD ASHFAQ*1 FAIZA KHAN1, SOHAIB AFZAAL1, UMMAD HUSSAIN1, MUBASSHIR HUSSAIN1, RASHID MUKHTAR BALAL2 & MUHAMMAD SALEEM HAIDER1 1 Institute of Agricultural Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan. 2Department of Horticulture, University of Sargodha, Sargodha, Pakistan ABSTRACT Endophytes have always been a topic of interest for researchers due to their wide variety of benefits to their hosts and their diversity of geographical distribution. In this study, bacterial endophytes were isolated from the leaf midrib of different varieties of citrus cultivated in the Sargodha region of Punjab Pakistan. The endophytic bacterial community associated with citrus was characterized and screened for antifungal activity against Alternaria solani which causes losses to crops. A total of twelve strains were identified based on morphological and biochemical tests following Bergey’s manual of systematic bacteriology. The antagonistic potential of bacterial endophytes to A. solani was explored using the agar absorption method. This study showed the antifungal potential of Pantoea sp. (35.66%), Ensifer adhaerens (35.33%), Citrobacter diversus (33.03%), and Azotobacter nigricans (31.56%) to check the growth of pathogenic fungi compared to controls. Aureobacterium liquifaciens (27.66%), Acinetobacter sp. (25.66%), Bordetella pertussis (26.63%) also showed equal potential for inhibition. In contrast remaining isolates Enterobacter cloacae (19.33%), Azomonas agilis (17%) and Kurthia sp. (19%) were less efficient as compared to the others. -
Hoffman Dissertation.Pdf
Determining the spatial and seasonal influences of microbial community composition and structure from the Hawaiian anchialine ecosystem by Stephanie Kimie Hoffman A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama December 10, 2016 Keywords: anchialine, microbial ecology, Hawaii, laminated mat, spatial variation, seasonal variation Copyright 2016 by Stephanie Kimie Hoffman Approved by Scott R Santos, Chair, Professor of Biological Sciences Mark R Liles, Professor of Biological Sciences Todd D Steury, Associate Professor of Wildlife Sciences Robert S Boyd, Professor and Undergraduate Program Officer of Biological Sciences Abstract Characterized as coastal bodies of water lacking surface connections to the ocean but with subterranean connections to the ocean and groundwater, habitats belonging to the anchialine ecosystem occur worldwide in primarily tropical latitudes. Such habitats contain tidally fluctuating complex physical and chemical clines and great species richness and endemism. The Hawaiian Archipelago hosts the greatest concentration of anchialine habitats globally, and while the endemic atyid shrimp and keystone grazer Halocaridina rubra has been studied, little work has been conducted on the microbial communities forming the basis of this ecosystem’s food web. Thus, this dissertation seeks to fill the knowledge gap regarding the endemic microbial communities in the Hawaiian anchialine ecosystem, particularly regarding spatial and seasonal influences on community diversity, composition, and structure. Briefly, Chapter 1 introduces the anchialine ecosystem and specific aims of this dissertation. In Chapter 2, environmental factors driving diversity and spatial variation among Hawaiian anchialine microbial communities are explored. Specifically, each sampled habitat was influenced by a unique combination of environmental factors that correlated with correspondingly unique microbial communities. -
Supplemental Information Supplemental Text Math for Back
Supplemental Information Supplemental Text Math for back calculating the per-cell division rates in Henson et al. 2018 assuming 15%--55% viability. "# Denote the initial cell count as �!, and the cell count in � generation as�$. If all the cells are viable, per each generation, all the cells are doubling: �$ = �$%& ⋅ 2 (eq. S1.1) And therefore, after �generations, the cell count �$would be: $ �$ = �! ⋅ 2 (eq. S1.2) When not all the cells are viable, for each generation, instead of simply doubling the whole population, only a portion of the cells (denoted as� < 1) replicates. In this case: �$ = �$%& ⋅ (1 + �) (eq. S1.3) Here we can see that (eq. 3.1) is actually a special case of (eq. 3.3), when � = 1, �$ = �$%& ⋅ (1 + 1) = �$%& ⋅ 2 When � < 1, after � generations: $ �$ = �! ⋅ (1 + �) (eq. S1.4) Denoting the total time to get � generations as �, which means the number of generations per unit time, also known as the per-cell division rate, is � = �/�. Rewriting (eq. 3.4), we have: '⋅" '⋅)*+!(&-.)⋅" �$ = �! ⋅ (1 + �) = �! ⋅ 2 (eq. S1.5) According to (eq. 3.5), a cell population of �viability and � per cell division rate, the population division rate is: �0*01)2"3*$ = � ⋅ ���4(1 + �) (eq. S1.6) %& Henson et al. 2018 show that the optimal population division rate of SAR11 LD12 is �0*01)2"3*$ = 0.5 ��� , assuming the viability of LD12 is � = 0.15, by plugging in these two numbers to (eq. S1.6), we can get the per-cell division rate of LD12 is: � = �0*01)2"3*$/���4(1 + �) %& = 0.5 ��� /���4(1 + 0.15) = 0.5 ���%&/0.20163 = 2.48 ���%& If assuming � = 0.55, � = 0.79 ���%&. -
Hydrogenophaga Defluvii Sp. Nov. and Hydrogenophaga Atypica Sp. Nov
International Journal of Systematic and Evolutionary Microbiology (2005), 55, 341–344 DOI 10.1099/ijs.0.03041-0 Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge Peter Ka¨mpfer,1 Renate Schulze,2 Udo Ja¨ckel,1 Khursheed A. Malik,3 Rudolf Amann4 and Stefan Spring3 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, 35392 Giessen, Peter Ka¨mpfer Germany peter.kaempfer@agrar. 2BRAIN Aktiengesellschaft, 64673 Zwingenberg, Germany uni-giessen.de 3DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124 Braunschweig, Germany 4Max-Planck-Institut fu¨r Marine Mikrobiologie, Celsiusstraße 1, 28359 Bremen, Germany Two Gram-negative, oxidase-positive rods (strains BSB 9.5T and BSB 41.8T) isolated from wastewater were studied using a polyphasic approach. 16S rRNA gene sequence comparisons demonstrated that both strains cluster phylogenetically within the family Comamonadaceae: the two strains shared 99?9 % 16S rRNA gene sequence similarity and were most closely related to the type strains of Hydrogenophaga palleronii (98?5 %) and Hydrogenophaga taeniospiralis (98?0 %). The fatty acid patterns and substrate-utilization profiles displayed similarity to the those of the five Hydrogenophaga species with validly published names, although clear differentiating characteristics were also observed. The two strains showed DNA–DNA hybridization values of 51 % with respect to each other. No close similarities to any other Hydrogenophaga species were detected in hybridization experiments with the genomic DNAs. On the basis of these results, two novel Hydrogenophaga species, Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov. are proposed, with BSB 9.5T (=DSM 15341T=CIP 108119T) and BSB 41.8T (=DSM 15342T=CIP 108118T) as the respective type strains. -
Identification of Microbiological Activities in Wet Flue Gas Desulfurization Systems
fmicb-12-675628 June 23, 2021 Time: 17:59 # 1 ORIGINAL RESEARCH published: 28 June 2021 doi: 10.3389/fmicb.2021.675628 Identification of Microbiological Activities in Wet Flue Gas Desulfurization Systems Gregory Martin1†, Shagun Sharma1,2, William Ryan1, Nanda K. Srinivasan3 and John M. Senko1,2,4* 1 Department of Biology, The University of Akron, Akron, OH, United States, 2 Integrated Bioscience Program, The University of Akron, Akron, OH, United States, 3 Electric Power Research Institute, Palo Alto, CA, United States, 4 Department of Geosciences, The University of Akron, Akron, OH, United States Thermoelectric power generation from coal requires large amounts of water, much of Edited by: which is used for wet flue gas desulfurization (wFGD) systems that minimize sulfur Anna-Louise Reysenbach, emissions, and consequently, acid rain. The microbial communities in wFGDs and Portland State University, throughout thermoelectric power plants can influence system performance, waste United States processing, and the long term stewardship of residual wastes. Any microorganisms Reviewed by: Nils-Kaare Birkeland, that survive in wFGD slurries must tolerate high total dissolved solids concentrations University of Bergen, Norway (TDS) and temperatures (50–60◦C), but the inocula for wFGDs are typically from Hannah Schweitzer, UiT The Arctic University of Norway, fresh surface waters (e.g., lakes or rivers) of low TDS and temperatures, and whose Norway activity might be limited under the physicochemically extreme conditions of the wFGD. *Correspondence: To determine the extents of microbiological activities in wFGDs, we examined the John M. Senko microbial activities and communities associated with three wFGDs. O consumption [email protected] 2 ◦ † Present address: rates of three wFGD slurries were optimal at 55 C, and living cells could be detected Gregory Martin, microscopically, indicating that living and active communities of organisms were present Division of Plant and Soil Sciences, in the wFGD and could metabolize at the high temperature of the wFGD. -
Transfer of Several Phytopathogenic Pseudomonas Species to Acidovorax As Acidovorax Avenae Subsp
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1992, p. 107-119 Vol. 42, No. 1 0020-7713/92/010107-13$02 .OO/O Copyright 0 1992, International Union of Microbiological Societies Transfer of Several Phytopathogenic Pseudomonas Species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov. , Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci A. WILLEMS,? M. GOOR, S. THIELEMANS, M. GILLIS,” K. KERSTERS, AND J. DE LEY Laboratorium voor Microbiologie en microbiele Genetica, Rijksuniversiteit Gent, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium DNA-rRNA hybridizations, DNA-DNA hybridizations, polyacrylamide gel electrophoresis of whole-cell proteins, and a numerical analysis of carbon assimilation tests were carried out to determine the relationships among the phylogenetically misnamed phytopathogenic taxa Pseudomonas avenue, Pseudomonas rubrilineans, “Pseudomonas setariae, ” Pseudomonas cattleyae, Pseudomonas pseudoalcaligenes subsp. citrulli, and Pseudo- monas pseudoalcaligenes subsp. konjaci. These organisms are all members of the family Comamonadaceae, within which they constitute a separate rRNA branch. Only P. pseudoalcaligenes subsp. konjaci is situated on the lower part of this rRNA branch; all of the other taxa cluster very closely around the type strain of P. avenue. When they are compared phenotypically, all of the members of this rRNA branch can be differentiated from each other, and they are, as a group, most closely related to the genus Acidovorax. DNA-DNA hybridization experiments showed that these organisms constitute two genotypic groups. We propose that the generically misnamed phytopathogenic Pseudomonas species should be transferred to the genus Acidovorax as Acidovorax avenue and Acidovorax konjaci. Within Acidovorax avenue we distinguished the following three subspecies: Acidovorax avenue subsp.