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Autotrophy in Groundwater Ecosystems
Dissertation der Fakultät für Biologie der Ludwig-Maximilians-Universität München Autotrophy in Groundwater Ecosystems Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades vorgelegt von Claudia Sabine Kellermann aus München München im November 2008 1. Gutachter: Prof. Dr. Anton Hartmann, LMU München 2. Gutachter: Prof. Dr. Dirk Schüler, LMU München Tag der Abgabe: 06.11.2008 Tag des Promotionskolloquiums: 15.07.2009 Publications originating from this Thesis Chapter 2 Kellermann, C & Griebler, C (2008) Thiobacillus thiophilus D24TNT sp. nov., a chemolithoautotrophic, thiosulfate-oxidizing bacterium isolated from contaminated aquifer sediments. International Journal of Systematic and Evolutionary Microbiology (IJSEM), 59: 583-588 Chapter 3 Kellermann, C, Selesi, D, Hartmann, A, Lee, N, Hügler, M, Esperschütz, J, & Griebler, C (2008) Chemolithoautotrophy in an organically polluted aquifer – Potential for CO2 fixation and in situ bacterial autotrophic activity. (in preparation) Contributions Chapter 3 Enzyme assays were performed in cooperation with Dr. Michael Hügler at the IFM- GEOMAR, Kiel, Germany. Chapter 4 FISH-MAR analysis was performed in cooperation with Prof. Dr. Natuschka Lee at the Technical University Munich, Germany. Enzyme assays were performed in cooperation with Dr. Michael Hügler at the IFM-GEOMAR, Kiel, Germany. PLFA analysis was performed by Dr. Jürgen Esperschütz at the Institute of Soil Ecology, Helmholtz Center Munich, Germany. I hereby confirm the above statements Claudia Kellermann Prof. Dr. Anton Hartmann Autotrophy in Groundwater Ecosystems Claudia Kellermann Abstract: The major role in global net CO2 fixation plays photosynthesis of green plants, algae and cyanobacteria, but other microorganisms are also important concerning autotrophy; i.e. autotrophic microorganisms can be found in most bacterial groups (Eubacteria) and there are even numerous representatives within the Archaea. -
Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Robust Taxonomic Classification of Uncharted Microbial Sequences and Bins with CAT and BAT
bioRxiv preprint doi: https://doi.org/10.1101/530188; this version posted January 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT F.A. Bastiaan von Meijenfeldt1,†, Ksenia Arkhipova1,†, Diego D. Cambuy1, Felipe H. Coutinho2,3, Bas E. Dutilh1,2,* 1 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, The Netherlands. 2 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. 3 Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. * To whom correspondence should be addressed. Tel: +31 30 253 4212; Email: [email protected]. † These authors contributed equally to this work. Present Address: [Felipe H. Couthinho], Evolutionary Genomics Group, Departamento de Produccíon y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain. ABSTRACT Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high- quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity. -
Identification of Pasteurella Species and Morphologically Similar Organisms
UK Standards for Microbiology Investigations Identification of Pasteurella species and Morphologically Similar Organisms Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 28 © Crown copyright 2015 Identification of Pasteurella species and Morphologically Similar Organisms Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 28 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Pasteurella species and Morphologically Similar Organisms Contents ACKNOWLEDGMENTS ......................................................................................................... -
Acholeplasma Florum, a New Species Isolated from Plants? R
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1984, p. 11-15 Vol. 34, No. 1 0020-7713/84/010011-05$02.OO/O Copyright 0 1984, International Union of Microbiological Societies Acholeplasma florum, a New Species Isolated from Plants? R. E. McCOY,l* H. G. BASHAM,' J. G. TULLY,* D. L. ROSE,2 P. CARLE,3 AND J. M. BOVE3 University of Florida Agricultural Research and Education Center, Fort Lauderdale, Florida 33314'; Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Frederick, Maryland 21 70i2;and lnstitut National de la Recherche Agronomique, Pont de la Maye 33140, France3 Three acholeplasmas isolated from floral surfaces of healthy plants in Florida were found to be similar in their biochemical and serological properties. These organisms did not require serum or cholesterol for growth, although addition of some supplementary fatty acids (as represented by Tween 80) was necessary for growth to occur in serum-free medium. The three strains possessed biochemical properties typical of the Acholeplasmataceae and were distinguished from the nine previously recognized Acholeplasma species by serological and deoxyribopucleic acid-deoxyribonucleic acid hybridization techniques. The genome molec- ular weight of the three Acholeplasma strains was lo9, and the guanine-plus-cytosine content of the deoxyribonucleic acid was 27 to 28 mol%. On the basis of these results and other morphological, biological, and serological properties, we propose that these organisms represent a new species, Acholeplasmaflorurn. Strain L1 (= ATCC 33453) is the type strain. Plant surfaces, particularly flowers, have recently been Media and cultivation procedures. Isolates were routinely proven to be fertile sites for isolation of members of the grown in MC broth or in the serum fraction medium de- Mycoplasrnatales (5, 11-13, 26). -
Acetobacter Sacchari Sp. Nov., for a Plant Growth-Promoting Acetic Acid Bacterium Isolated in Vietnam
Annals of Microbiology (2019) 69:1155–11631163 https://doi.org/10.1007/s13213-019-01497-0 ORIGINAL ARTICLE Acetobacter sacchari sp. nov., for a plant growth-promoting acetic acid bacterium isolated in Vietnam Huong Thi Lan Vu1,2 & Pattaraporn Yukphan3 & Van Thi Thu Bui1 & Piyanat Charoenyingcharoen3 & Sukunphat Malimas4 & Linh Khanh Nguyen1 & Yuki Muramatsu5 & Naoto Tanaka6 & Somboon Tanasupawat7 & Binh Thanh Le2 & Yasuyoshi Nakagawa5 & Yuzo Yamada3,8,9 Received: 21 January 2019 /Accepted: 7 July 2019 /Published online: 18 July 2019 # Università degli studi di Milano 2019 Abstract Purpose Two bacterial strains, designated as isolates VTH-Ai14T and VTH-Ai15, that have plant growth-promoting ability were isolated during the study on acetic acid bacteria diversity in Vietnam. The phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates were located closely to Acetobacter nitrogenifigens RG1T but formed an independent cluster. Methods The phylogenetic analysis based on 16S rRNA gene and three housekeeping genes’ (dnaK, groEL, and rpoB) sequences were analyzed. The genomic DNA of the two isolates, VTH-Ai14T and VTH-Ai15, Acetobacter nitrogenifigens RG1T, the closest phylogenetic species, and Acetobacter aceti NBRC 14818T were hybridized and calculated the %similarity. Then, phenotypic and chemotaxonomic characteristics were determined for species’ description using the conventional method. Results The 16S rRNA gene and concatenated of the three housekeeping genes phylogenetic analysis suggests that the two isolates were constituted in a species separated from Acetobacter nitrogenifigens, Acetobacter aceti,andAcetobacter sicerae. The two isolates VTH-Ai14T and VTH-Ai15 showed 99.65% and 98.65% similarity of 16S rRNA gene when compared with Acetobacter nitrogenifigens and Acetobacter aceti and they were so different from Acetobacter nitrogenifigens RG1T with 56.99 ± 3.6 and 68.15 ± 1.8% in DNA-DNA hybridization, when isolates VTH-Ai14T and VTH-Ai15 were respectively labeled. -
Achromobacter Buckle Infection Diagnosed by a 16S Rdna Clone
Hotta et al. BMC Ophthalmology 2014, 14:142 http://www.biomedcentral.com/1471-2415/14/142 CASE REPORT Open Access Achromobacter buckle infection diagnosed by a 16S rDNA clone library analysis: a case report Fumika Hotta1†, Hiroshi Eguchi1*, Takeshi Naito1†, Yoshinori Mitamura1†, Kohei Kusujima2† and Tomomi Kuwahara3† Abstract Background: In clinical settings, bacterial infections are usually diagnosed by isolation of colonies after laboratory cultivation followed by species identification with biochemical tests. However, biochemical tests result in misidentification due to similar phenotypes of closely related species. In such cases, 16S rDNA sequence analysis is useful. Herein, we report the first case of an Achromobacter-associated buckle infection that was diagnosed by 16S rDNA sequence analysis. This report highlights the significance of Achromobacter spp. in device-related ophthalmic infections. Case presentation: A 56-year-old woman, who had received buckling surgery using a silicone solid tire for retinal detachment eighteen years prior to this study, presented purulent eye discharge and conjunctival hyperemia in her right eye. Buckle infection was suspected and the buckle material was removed. Isolates from cultures of preoperative discharge and from deposits on the operatively removed buckle material were initially identified as Alcaligenes and Corynebacterium species. However, sequence analysis of a 16S rDNA clone library using the DNA extracted from the deposits on the buckle material demonstrated that all of the 16S rDNA sequences most closely matched those of Achromobacter spp. We concluded that the initial misdiagnosis of this case as an Alcaligenes buckle infection was due to the unreliability of the biochemical test in discriminating Achromobacter and Alcaligenes species due to their close taxonomic positions and similar phenotypes. -
Genomic Islands in Mycoplasmas
G C A T T A C G G C A T genes Review Genomic Islands in Mycoplasmas Christine Citti * , Eric Baranowski * , Emilie Dordet-Frisoni, Marion Faucher and Laurent-Xavier Nouvel Interactions Hôtes-Agents Pathogènes (IHAP), Université de Toulouse, INRAE, ENVT, 31300 Toulouse, France; [email protected] (E.D.-F.); [email protected] (M.F.); [email protected] (L.-X.N.) * Correspondence: [email protected] (C.C.); [email protected] (E.B.) Received: 30 June 2020; Accepted: 20 July 2020; Published: 22 July 2020 Abstract: Bacteria of the Mycoplasma genus are characterized by the lack of a cell-wall, the use of UGA as tryptophan codon instead of a universal stop, and their simplified metabolic pathways. Most of these features are due to the small-size and limited-content of their genomes (580–1840 Kbp; 482–2050 CDS). Yet, the Mycoplasma genus encompasses over 200 species living in close contact with a wide range of animal hosts and man. These include pathogens, pathobionts, or commensals that have retained the full capacity to synthesize DNA, RNA, and all proteins required to sustain a parasitic life-style, with most being able to grow under laboratory conditions without host cells. Over the last 10 years, comparative genome analyses of multiple species and strains unveiled some of the dynamics of mycoplasma genomes. This review summarizes our current knowledge of genomic islands (GIs) found in mycoplasmas, with a focus on pathogenicity islands, integrative and conjugative elements (ICEs), and prophages. Here, we discuss how GIs contribute to the dynamics of mycoplasma genomes and how they participate in the evolution of these minimal organisms. -
The Availability of Purine Nucleotides Regulates Natural Competence by Controlling Translation of the Competence Activator Sxy
Molecular Microbiology (2013) ■ doi:10.1111/mmi.12245 The availability of purine nucleotides regulates natural competence by controlling translation of the competence activator Sxy Sunita Sinha,* Joshua Mell and Rosemary Redfield (transformation), natural transformation is a major mecha- Department of Zoology, University of British Columbia, nism of genetic exchange, shaping bacterial genomes and Vancouver V6T 3Z4, Canada. spreading alleles that increase bacterial survival and virulence (Domingues et al., 2012; Livermore, 2012). However, most DNA taken up by competent cells is Summary degraded, providing nucleotides, elements (C, N, P) and Many bacteria are naturally competent, able to bind energy, but no genetic information (Pifer and Smith, 1985; and take up DNA from their extracellular environment. Stewart and Carlson, 1986). This suggests that DNA This DNA can serve as a significant source of nutri- uptake could make a significant contribution to cellular ents, in addition to providing genetic material for re- metabolism. However, although nutritional signals affect combination. The regulation of competence in several competence development in most model systems, their model organisms highlights the importance of this roles are often thought to be indirect (Solomon and nutritional function, although it has often been over- Grossman, 1996; Macfadyen, 2000; Finkel and Kolter, looked. Natural competence is induced by starvation 2001; Palchevskiy and Finkel, 2006; Bosse et al., 2009; in Haemophilus influenzae, the model for competence Johnsborg and Havarstein, 2009; Kristensen et al., 2012). regulation in the gamma-proteobacteria. This induc- Nutritional signals play a prominent role in competence tion depends on the activation of the global metabolic of Haemophilus influenzae, the model for gamma- regulator CRP, which occurs upon depletion of phos- proteobacteria. -
Characterization of Antibiotic Resistance Genes in the Species of the Rumen Microbiota
ARTICLE https://doi.org/10.1038/s41467-019-13118-0 OPEN Characterization of antibiotic resistance genes in the species of the rumen microbiota Yasmin Neves Vieira Sabino1, Mateus Ferreira Santana1, Linda Boniface Oyama2, Fernanda Godoy Santos2, Ana Júlia Silva Moreira1, Sharon Ann Huws2* & Hilário Cuquetto Mantovani 1* Infections caused by multidrug resistant bacteria represent a therapeutic challenge both in clinical settings and in livestock production, but the prevalence of antibiotic resistance genes 1234567890():,; among the species of bacteria that colonize the gastrointestinal tract of ruminants is not well characterized. Here, we investigate the resistome of 435 ruminal microbial genomes in silico and confirm representative phenotypes in vitro. We find a high abundance of genes encoding tetracycline resistance and evidence that the tet(W) gene is under positive selective pres- sure. Our findings reveal that tet(W) is located in a novel integrative and conjugative element in several ruminal bacterial genomes. Analyses of rumen microbial metatranscriptomes confirm the expression of the most abundant antibiotic resistance genes. Our data provide insight into antibiotic resistange gene profiles of the main species of ruminal bacteria and reveal the potential role of mobile genetic elements in shaping the resistome of the rumen microbiome, with implications for human and animal health. 1 Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. 2 Institute for Global Food Security, School of Biological -
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DISEASES OF AQUATIC ORGANISMS Vol. 3: 97-100, 1987 Published December 14 Dis. aquat. Org. l Screening of Norwegian lobsters Homarus gammarus for the lobster pathogen Aerococcus virid ans Ragnhild wiikl, Emmy Egidiusl, Jostein ~oksayr~ ' Institute of Marine Research, Directorate of Fisheries, PO Box 2906, N-5011 Bergen-Nordnes. Norway ' Department of Microbiology and Plant Physiology. University of Bergen. N-5014 Bergen-University, Norway ABSTRACT: Hemolymph samples drawn from 3044 lobsters trapped along the southwestern part of the Norwegian coast in the period 1981 to 1984 were individually examined for Aerococcus viridans, the causative agent of gaffkemia. In 1981, one of 779 hemolymph samples was positive with respect to the bacterium. During the period 1982 to 1984, 2265 lobsters were examined and found negative for A. viridans. These results, together with the fact that gaffkemia has not been reported in the region since 1980, suggest that the disease is not enzootic in these waters. Because of the high survival capacity of the lobster pathogen, strong measures with respect to disinfection of ponds and tanks are recom- mended following outbreaks of gaffkemia. INTRODUCTION Kvits~y,an island situated about 25 km northwest of Stavanger. Mortalities among the imported lobsters, Gaffkemia is an infection of lobsters caused by the however, continued, and gaffkemia was diagnosed as bacterium Aerococcus viridans (Evans 1974). The dis- the cause (Hbstein et al. 1977). ease can cause heavy mortalities among both Homarus New outbreaks of gaffkemia occurred in Stavanger americanus H. Milne Edwards 1837 and H, gammarus and at Kvits~yIn 1977 and 1980; all 6 ponds in the area L. -
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.