Genome-Scale Data Suggest Reclassifications in the Leisingera
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<I>Euprymna Scolopes</I>
University of Connecticut OpenCommons@UConn Honors Scholar Theses Honors Scholar Program Spring 5-10-2009 Characterizing the Role of Phaeobacter in the Mortality of the Squid, Euprymna scolopes Brian Shawn Wong Won University of Connecticut - Storrs, [email protected] Follow this and additional works at: https://opencommons.uconn.edu/srhonors_theses Part of the Cell Biology Commons, Molecular Biology Commons, and the Other Animal Sciences Commons Recommended Citation Wong Won, Brian Shawn, "Characterizing the Role of Phaeobacter in the Mortality of the Squid, Euprymna scolopes" (2009). Honors Scholar Theses. 67. https://opencommons.uconn.edu/srhonors_theses/67 Characterizing the Role of Phaeobacter in the Mortality of the Squid, Euprymna scolopes . Author: Brian Shawn Wong Won Advisor: Spencer V. Nyholm Ph.D. University of Connecticut Honors Program Date submitted: 05/11/09 1 Abstract The subject of our study is the Hawaiian bobtail squid, Euprymna scolopes , which is known for its model symbiotic relationship with the bioluminescent bacterium, Vibrio fischeri . The interactions between E. scolopes and V. fischeri provide an exemplary model of the biochemical and molecular dynamics of symbiosis since both members can be cultivated separately and V. fischeri can be genetically modified 1. However, in a laboratory setting, the mortality of embryonic E. scolopes can be a recurrent problem. In many of these fatalities, the egg cases display a pink-hued biofilm, and rosy pigmentation has also been noted in the deaths of several adult squid. To identify the microbial components of this biofilm, we cloned and sequenced the 16s ribosomal DNA gene from pink, culture-grown isolates from infected egg cases and adult tissues. -
Dual Oxidase Gene Duox and Toll-Like Receptor 3 Gene TLR3 in the Toll
bioRxiv preprint doi: https://doi.org/10.1101/844696; this version posted November 15, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. 1 Dual oxidase gene Duox and Toll-like receptor 3 gene TLR3 2 in the Toll pathway suppress zoonotic pathogens through 3 regulating the intestinal bacterial community homeostasis in 4 Hermetia illucens L. 5 Yaqing Huang1, Yongqiang Yu1, Shuai Zhan2, Jeffery K. Tomberlin3, Dian Huang1, 6 Minmin Cai1, Longyu Zheng1, Ziniu Yu1, Jibin Zhang1* 7 1State Key Laboratory of Agricultural Microbiology, National Engineering Research 8 Center of Microbial Pesticides, College of Life Science and Technology, Huazhong 9 Agricultural University, Wuhan, P.R. China 430070. 10 2 Institute of Plant Physiology & Ecology, SIBS, CAS, China 200032. 11 3Department of Entomology, Texas A&M University, USA; 12 * Correspondence: 13 Professor Jibin Zhang 14 [email protected] 15 1 bioRxiv preprint doi: https://doi.org/10.1101/844696; this version posted November 15, 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 4.0 International license. 16 Abstract: 17 Black soldier fly (BSF; Hermetia illucens L.) larvae can convert fresh pig manure 18 into protein and fat-rich biomass, which can then be used as livestock feed. Currently, 19 it is the only insect approved for such purposes in Europe, Canada, and the USA. -
Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter
GBE Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter Heike M. Freese1,*, Johannes Sikorski1, Boyke Bunk1,CarmenScheuner1, Jan P. Meier-Kolthoff1, Cathrin Spro¨er1,LoneGram2,andJo¨rgOvermann1,3 1Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany 2Department of Biotechnology and Bioengineering, Technical University of Denmark, Lyngby, Denmark 3Institute of Microbiology, University Braunschweig, Germany *Corresponding author: E-mail: [email protected]. Accepted: November 27, 2017 Data deposition: This project has been deposited at GenBank under the accessions CP010588 - CP010775, CP010784 - CP010791, CP010805 - CP010810, KY357362 - KY357447. Abstract The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome. The flexible gene pool is constantly but slightly expanding across all Phaeobacter lineages. The horizontally transferred genes mostly originated from bacteria of the Roseobacter group and horizontal transfer most likely was mediated by gene transfer agents. No evidence for geographic isolation and habitat specificity of the different phylogenomic Phaeobacter clades was detected based on the sources of isolation. In contrast, the functional gene repertoire and physiological traits of different phylogenomic Phaeobacter clades were sufficiently distinct to suggest an adaptation to an associated lifestyle with algae, to additional nutrient sources, or toxic heavy metals. -
Isolation of Phaeobacter Sp. from Larvae of Atlantic Bonito
microorganisms Article Isolation of Phaeobacter sp. from Larvae of Atlantic Bonito (Sarda sarda) in a Mesocosmos Unit, and Its Use for the Rearing of European Seabass Larvae (Dicentrarchus labrax L.) Pavlos Makridis 1,* , Fotini Kokou 2 , Christos Bournakas 1, Nikos Papandroulakis 3 and Elena Sarropoulou 3 1 Department of Biology, University of Patras, Rio 26504 Patras, Greece; [email protected] 2 Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University and Research, 6700AH Wageningen, The Netherlands; [email protected] 3 Biotechnology, and Aquaculture, Hellenic Center for Marine Research, Institute of Marine Biology, P.O. Box 2214, 71003 Heraklion Crete, Greece; [email protected] (N.P.); [email protected] (E.S.) * Correspondence: [email protected]; Tel.: +30-2610-969224 Abstract: The target of this study was to use indigenous probiotic bacteria in the rearing of seabass larvae. A Phaeobacter sp. strain isolated from bonito yolk-sac larvae (Sarda sarda) and identified by amplification of 16S rDNA showed in vitro inhibition against Vibrio anguillarum. This Phaeobacter sp. strain was used in the rearing of seabass larvae (Dicentrarchus labrax L.) in a large-scale trial. The survival of seabass after 60 days of rearing and the specific growth rate at the late exponential growth phase were significantly higher in the treatment receiving probiotics (p < 0.05). Microbial community richness as determined by denaturing gradient gel electrophoresis (DGGE) showed an increase in bacterial diversity with fish development. Changes associated with the administration of probiotics were observed 11 and 18 days after hatching but were not apparent after probiotic administration Citation: Makridis, P.; Kokou, F.; stopped. -
Isolation of an Antimicrobial Compound Produced by Bacteria Associated with Reef-Building Corals
Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals Jean-Baptiste Raina1,2,3,4,5, Dianne Tapiolas2, Cherie A. Motti2, Sylvain Foret3,6, Torsten Seemann7, Jan Tebben8,9, Bette L. Willis3,4 and David G. Bourne2,4 1 Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, Australia 2 Australian Institute of Marine Science, Townsville, QLD, Australia 3 Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia 4 Marine Biology and Aquaculture, College of Science and Engineering, James Cook University of North Queensland, Townsville, QLD, Australia 5 AIMS@JCU, James Cook University, Townsville, QLD, Australia 6 Research School of Biology, Australian National University, Canberra, ACT, Australia 7 Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Victoria, Australia 8 Section Chemical Ecology, Alfred Wegener Institute, Bremerhaven, Germany 9 University of New South Wales, Sydney, NSW, Australia ABSTRACT Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear Submitted 15 May 2016 magnetic resonance (NMR) and mass spectrometry (MS), identified the Accepted 19 July 2016 antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely Published 18 August 2016 derived from DMSP catabolism. -
Phaeobacter Leonis Sp. Nov., an Alphaproteobacterium
International Journal of Systematic and Archimer Evolutionary Microbiology http://archimer.ifremer.fr September 2013, Volume 63, Pages 3301-3306 http://dx.doi.org/10.1099/ijs.0.046128-0 © 2013 IUMS Printed in Great Britain Phaeobacter leonis sp. nov., an alphaproteobacterium from is available on the publisher Web site Webpublisher the on available is Mediterranean Sea sediments Frédéric Gaboyer1,2,3, Brian J. Tindall4, Maria-Cristina Ciobanu1,2,3, Frédérique Duthoit1,2,3, Marc Le Romancer1,2,3 and Karine Alain1,2,3 authenticated version authenticated - 1 Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) – UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France 2 CNRS, IUEM – UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France 3 Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France 4 DSMZ – Deutsche Sammlung von Mikroorganismem und Zellkulturen Gmbh. Inhoffenstr. 7bN D-38124 Braunschweig. Germany *: Corresponding author : Frédéric Gaboyer, email address : [email protected] owing peer review. The definitive publisherdefinitive The review. owing peer Abstract: A novel Gram-stain-negative, strictly aerobic, heterotrophic bacterium, designated 306T, was isolated from near-surface (109 cm below the sea floor) sediments of the Gulf of Lions, in the Mediterranean Sea. Strain 306T grew at temperatures between 4 and 32 °C (optimum 17–22 °C), from pH 6.5 to 9.0 (optimum 8.0–9.0) and between 0.5 and 6.0 % (w/v) NaCl (optimum 2.0 %). -
1 Monitoring of the Bioencapsulation of a Probiotic Phaeobacter Strain In
*Manuscript Click here to view linked References 1 2 Monitoring of the bioencapsulation of a probiotic Phaeobacter strain in the rotifer 3 Brachionus plicatilis using denaturing gradient gel electrophoresis 4 5 José Pintado1*, María Pérez-Lorenzo1,2, Antonio Luna-González1,3, Carmen G. Sotelo1, 6 María J. Prol1 and Miquel Planas1 7 8 1Instituto de Investigacións Mariñas (CSIC), Eduardo Cabello nº 6, 36208 Vigo, 9 Galicia, Spain. 10 2 Present address: Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 11 36310 Vigo, Galicia, Spain. 12 3 Present address: Centro Interdisciplinario de Investigación para el Desarrollo Integral 13 Regional-Instituto Politécnico Nacional, Unidad Sinaloa. Boulevard Juan de Dios Bátiz 14 Paredes 250, Guasave, Sinaloa 81101, México 15 16 17 *Corresponding author: Phone +34986231930. Fax +34986292762. E-mail address: 18 [email protected]. 19 20 Abstract 21 22 The bioencapsulation of the probiotic bacteria Phaeobacter 27-4 in the rotifer 23 Brachionus plicatilis was monitored by culture methods and denaturing gradient gel 24 electrophoresis (DGGE) of PCR-amplified 16S rDNA. 25 In a first experiment, the permanence of the probiotic bacteria in clear water and green 26 water was studied. Phaeobacter 27-4 added to the water of the tanks (107 CFU ml-1) 27 remained at levels around 106 CFU ml-1 for 72 h and was not affected by the presence of 28 the algae added (Isochrysis galbana, 105 cells ml-1). The DGGE fingerprints showed a 29 temporal predominance of the probiont in the water and the presence of bacteria 30 belonging to the Flavobacteria, -proteobacteria, and Sphingobacteria groups. -
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; -
Diatom Modulation of Select Bacteria Through Use of Two Unique Secondary Metabolites
Diatom modulation of select bacteria through use of two unique secondary metabolites Ahmed A. Shibla, Ashley Isaaca,b, Michael A. Ochsenkühna, Anny Cárdenasc,d, Cong Feia, Gregory Behringera, Marc Arnouxe, Nizar Droue, Miraflor P. Santosa,1, Kristin C. Gunsaluse,f, Christian R. Voolstrac,d, and Shady A. Amina,2 aMarine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates; bInternational Max Planck Research School of Marine Microbiology, University of Bremen, Bremen 28334, Germany; cDepartment of Biology, University of Konstanz, Konstanz 78467, Germany; dRed Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; eCenter for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates; and fCenter for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003 Edited by Edward F. DeLong, University of Hawaii at Manoa, Honolulu, HI, and approved September 10, 2020 (received for review June 12, 2020) Unicellular eukaryotic phytoplankton, such as diatoms, rely on shown to heavily rely on phycosphere DOM to support their microbial communities for survival despite lacking specialized growth (14, 15) and must use motility, chemotaxis, and/or at- compartments to house microbiomes (e.g., animal gut). Microbial tachment to chase and colonize the phycosphere (16). Recent communities have been widely shown to benefit from diatom research has shown that a variety of interactions spanning mu- excretions that accumulate within the microenvironment sur- tualism, commensalism, and parasitism occur between diatoms rounding phytoplankton cells, known as the phycosphere. -
Diversity of Arsenite Oxidase Gene and Arsenotrophic Bacteria in Arsenic
Sanyal et al. AMB Expr (2016) 6:21 DOI 10.1186/s13568-016-0193-0 ORIGINAL ARTICLE Open Access Diversity of arsenite oxidase gene and arsenotrophic bacteria in arsenic affected Bangladesh soils Santonu Kumar Sanyal1,3, Taslin Jahan Mou1,4, Ram Prosad Chakrabarty1, Sirajul Hoque2, M. Anwar Hossain1 and Munawar Sultana1* Abstract Arsenic (As) contaminated soils are enriched with arsenotrophic bacteria. The present study analyzes the microbiome and arsenotrophic genes-from As affected soil samples of Bhanga, Charvadrason and Sadarpur of Faridpur district in Bangladesh in summer (SFDSL1, 2, 3) and in winter (WFDSL1, 2, 3). Total As content of the soils was within the range of 3.24–17.8 mg/kg as per atomic absorption spectroscopy. The aioA gene, conferring arsenite [As (III)] oxidation, was retrieved from the soil sample, WFDSL-2, reported with As concentration of 4.9 mg/kg. Phylogenetic analysis revealed that the aioA genes of soil WFDSL-2 were distributed among four major phylogenetic lineages comprised of α, β, γ Proteobacteria and Archaea with a dominance of β Proteobacteria (56.67 %). An attempt to enrich As (III) metabolizing bacteria resulted 53 isolates. ARDRA (amplified ribosomal DNA restriction analysis) followed by 16S rRNA gene sequencing of the 53 soil isolates revealed that they belong to six genera; Pseudomonas spp., Bacillus spp., Brevibacillus spp., Delftia spp., Wohlfahrtiimonas spp. and Dietzia spp. From five different genera, isolates Delftia sp. A2i, Pseudomonas sp. A3i, W. chitiniclastica H3f, Dietzia sp. H2f, Bacillus sp. H2k contained arsB gene and showed arsenite tolerance up-to 27 mM. Phenotypic As (III) oxidation potential was also confirmed with the isolates of each genus and isolate Brevibacillus sp. -
Microbiome-Assisted Carrion Preservation Aids Larval Development in a Burying Beetle
Microbiome-assisted carrion preservation aids larval development in a burying beetle Shantanu P. Shuklaa,1, Camila Plataa, Michael Reicheltb, Sandra Steigerc, David G. Heckela, Martin Kaltenpothd, Andreas Vilcinskasc,e, and Heiko Vogela,1 aDepartment of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; bDepartment of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; cInstitute of Insect Biotechnology, Justus-Liebig-University of Giessen, 35392 Giessen, Germany; dEvolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, 55128 Mainz, Germany; and eDepartment Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, 35394 Giessen, Germany Edited by Nancy A. Moran, The University of Texas at Austin, Austin, TX, and approved September 18, 2018 (received for review July 30, 2018) The ability to feed on a wide range of diets has enabled insects to their larvae, thereby modifying the carcass substantially (12, 23, 26, diversify and colonize specialized niches. Carrion, for example, is 27). Application of oral and anal secretions is hypothesized to highly susceptible to microbial decomposers, but is kept palatable support larval development (27), to transfer nutritive enzymes (21, several days after an animal’s death by carrion-feeding insects. Here 28, 29), transmit mutualistic microorganisms to the carcass (10, 21, we show that the burying beetle Nicrophorus vespilloides preserves 22, 30), and suppress microbial competitors through their antimi- – carrion by preventing the microbial succession associated with car- crobial activity (11, 23, 31 34). The secretions inhibit several Gram- rion decomposition, thus ensuring a high-quality resource for their positive and Gram-negative bacteria, yeasts, and molds (11, 31, 35), developing larvae. -
The Porcine Nasal Microbiota with Particular Attention to Livestock-Associated Methicillin-Resistant Staphylococcus Aureus in Germany—A Culturomic Approach
microorganisms Article The Porcine Nasal Microbiota with Particular Attention to Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Germany—A Culturomic Approach Andreas Schlattmann 1, Knut von Lützau 1, Ursula Kaspar 1,2 and Karsten Becker 1,3,* 1 Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; [email protected] (A.S.); [email protected] (K.v.L.); [email protected] (U.K.) 2 Landeszentrum Gesundheit Nordrhein-Westfalen, Fachgruppe Infektiologie und Hygiene, 44801 Bochum, Germany 3 Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany * Correspondence: [email protected]; Tel.: +49-3834-86-5560 Received: 17 March 2020; Accepted: 2 April 2020; Published: 4 April 2020 Abstract: Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) remains a serious public health threat. Porcine nasal cavities are predominant habitats of LA-MRSA. Hence, components of their microbiota might be of interest as putative antagonistically acting competitors. Here, an extensive culturomics approach has been applied including 27 healthy pigs from seven different farms; five were treated with antibiotics prior to sampling. Overall, 314 different species with standing in nomenclature and 51 isolates representing novel bacterial taxa were detected. Staphylococcus aureus was isolated from pigs on all seven farms sampled, comprising ten different spa types with t899 (n = 15, 29.4%) and t337 (n = 10, 19.6%) being most frequently isolated. Twenty-six MRSA (mostly t899) were detected on five out of the seven farms. Positive correlations between MRSA colonization and age and colonization with Streptococcus hyovaginalis, and a negative correlation between colonization with MRSA and Citrobacter spp.