Glitter-Like Iridescence Within the Bacteroidetes Especially Cellulophaga Spp.: Optical Properties and Correlation with Gliding Motility
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CUED Phd and Mphil Thesis Classes
High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice. -
Inferring Gene Function from Evolutionary Change in Signatures
Krisko et al. Genome Biology 2014, 15:R44 http://genomebiology.com/2014/15/3/R44 RESEARCH Open Access Inferring gene function from evolutionary change in signatures of translation efficiency Anita Krisko1, Tea Copic1, Toni Gabaldón2,3,5, Ben Lehner3,4,5 and Fran Supek2,3,4* Abstract Background: The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the relative expression levels of genes, which can, uniquely, be quantified across the domains of life. Results: Here we describe a general statistical framework to exploit this phenomenon and to systematically associate genes with environments and phenotypic traits through changes in codon adaptation. By inferring evolutionary signatures of translation efficiency in 911 bacterial and archaeal genomes while controlling for confounding effects of phylogeny and inter-correlated phenotypes, we linked 187 gene families to 24 diverse phenotypic traits. A series of experiments in Escherichia coli revealed that 13/15, 19/23, and 3/6 gene families with changes in codon adaptation in aerotolerant, thermophilic, or halophilic microbes confer specific resistance to, respectively, hydrogen peroxide, heat, and high salinity. Further, we demonstrate experimentally that changes in codon optimality alone are sufficient to enhance stress resistance. Finally, we present evidence that multiple genes with altered codon optimality in aerobes confer oxidative stress resistance by controlling the levels of iron and NAD(P)H. Conclusions: Taken together, these results provide experimental evidence for a widespread connection between changes in translation efficiency and phenotypic adaptation. -
Genomic and Phenotypic Insights Into the Ecology of Arthrobacter from Antarctic Soils Melissa Dsouza1*, Michael W Taylor1, Susan J Turner1,2 and Jackie Aislabie3
Dsouza et al. BMC Genomics (2015) 16:36 DOI 10.1186/s12864-015-1220-2 RESEARCH ARTICLE Open Access Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils Melissa Dsouza1*, Michael W Taylor1, Susan J Turner1,2 and Jackie Aislabie3 Abstract Background: Members of the bacterial genus Arthrobacter are both readily cultured and commonly identified in Antarctic soil communities. Currently, relatively little is known about the physiological traits that allow these bacteria to survive in the harsh Antarctic soil environment. The aim of this study is to investigate if Antarctic strains of Arthrobacter owe their resilience to substantial genomic changes compared to Arthrobacter spp. isolated from temperate soil environments. Results: Quantitative PCR-based analysis revealed that up to 4% of the soil bacterial communities were comprised of Arthrobacter spp. at four locations in the Ross Sea Region. Genome analysis of the seven Antarctic Arthrobacter isolates revealed several features that are commonly observed in psychrophilic/psychrotolerant bacteria. These include genes primarily associated with sigma factors, signal transduction pathways, the carotenoid biosynthesis pathway and genes induced by cold-shock, oxidative and osmotic stresses. However, these genes were also identified in genomes of seven temperate Arthrobacter spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. Phenotypic characterisation revealed that Antarctic Arthrobacter isolates demonstrate significantly lower metabolic versatility and a narrower salinity tolerance range compared to temperate Arthrobacter species. Comparative analyses also revealed fewer protein-coding sequences and a significant decrease in genes associated with transcription and carbohydrate transport and metabolism in four of the seven Antarctic Arthrobacter isolates. -
1 Large-Scale Maps of Variable Infection Efficiencies in Aquatic Bacteroidetes Phage
1 Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage- 2 host model systems 3 Karin Holmfeldt1,2, Natalie Solonenko1,a, Cristina Howard-Varona1,a, Mario Moreno1, 4 Rex R. Malmstrom3, Matthew J. Blow3, Matthew B. Sullivan1,a,b 5 1Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 6 USA 7 2Centre for Ecology and Evolution in Microbial Model Systems, Department of Biology 8 and Environmental Sciences, Linnaeus University, Kalmar, Sweden 9 3DOE Joint Genome Institute, Walnut Creek, CA, USA 10 Current affiliation: Departments of aMicrobiology, and bCivil, Environmental and 11 Geodetic Engineering, The Ohio State University, Columbus, OH 12 * corresponding author: Karin Holmfeldt, Center for Ecology and Evolution in Microbial 13 Model Systems, Department of Biology and Environmental Sciences, Linnaeus 14 University, SE-391 82 Kalmar, Sweden. Phone nr +46-480-447310, Fax nr +46-480- 15 447305, email [email protected]. 16 17 Running title: Variable phage-host infection interactions 1 18 Summary 19 Microbes drive ecosystem functioning, and their viruses modulate these impacts through 20 mortality, gene transfer, and metabolic reprogramming. Despite the importance of virus- 21 host interactions and likely variable infection efficiencies of individual phages across 22 hosts, such variability is seldom quantified. Here we quantify infection efficiencies of 38 23 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage-host model 24 systems. Binary data revealed that some phages infected only one strain while others 25 infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 26 orders of magnitude, even among phages within one population. -
Targeting of Flavobacterium Johnsoniae Proteins for Secretion by the Type IX Secretion System Surashree Sunil Kulkarni University of Wisconsin-Milwaukee
University of Wisconsin Milwaukee UWM Digital Commons Theses and Dissertations May 2017 Targeting of Flavobacterium Johnsoniae Proteins for Secretion By the Type IX Secretion System Surashree Sunil Kulkarni University of Wisconsin-Milwaukee Follow this and additional works at: https://dc.uwm.edu/etd Part of the Microbiology Commons Recommended Citation Kulkarni, Surashree Sunil, "Targeting of Flavobacterium Johnsoniae Proteins for Secretion By the Type IX Secretion System" (2017). Theses and Dissertations. 1501. https://dc.uwm.edu/etd/1501 This Dissertation is brought to you for free and open access by UWM Digital Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of UWM Digital Commons. For more information, please contact [email protected]. TARGETING OF FLAVOBACTERIUM JOHNSONIAE PROTEINS FOR SECRETION BY THE TYPE IX SECRETION SYSTEM by Surashree S. Kulkarni A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Sciences at The University of Wisconsin-Milwaukee May 2017 ABSTRACT TARGETING OF FLAVOBACTERIUM JOHNSONIAE PROTEINS FOR SECRETION BY THE TYPE IX SECRETION SYSTEM by Surashree S. Kulkarni The University of Wisconsin-Milwaukee, 2017 Under the Supervision of Dr. Mark J. McBride Flavobacterium johnsoniae and many related bacteria secrete proteins across the outer membrane using the type IX secretion system (T9SS). Proteins secreted by T9SSs have amino-terminal signal peptides for export across the cytoplasmic membrane by the Sec system and carboxy-terminal domains (CTDs) targeting them for secretion across the outer membrane by the T9SS. Most but not all T9SS CTDs belong to family TIGR04183 (type A CTDs). -
Taxon-Specific Aerosolization of Bacteria and Viruses in An
ARTICLE DOI: 10.1038/s41467-018-04409-z OPEN Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm Jennifer M. Michaud1, Luke R. Thompson 2,3,4, Drishti Kaul5, Josh L. Espinoza5, R. Alexander Richter5, Zhenjiang Zech Xu2, Christopher Lee1, Kevin M. Pham1, Charlotte M. Beall6, Francesca Malfatti6,7, Farooq Azam6, Rob Knight 2,8,9, Michael D. Burkart 1, Christopher L. Dupont5 & Kimberly A. Prather1,6 1234567890():,; Ocean-derived, airborne microbes play important roles in Earth’s climate system and human health, yet little is known about factors controlling their transfer from the ocean to the atmosphere. Here, we study microbiomes of isolated sea spray aerosol (SSA) collected in a unique ocean–atmosphere facility and demonstrate taxon-specific aerosolization of bacteria and viruses. These trends are conserved within taxonomic orders and classes, and temporal variation in aerosolization is similarly shared by related taxa. We observe enhanced transfer into SSA of Actinobacteria, certain Gammaproteobacteria, and lipid-enveloped viruses; conversely, Flavobacteriia, some Alphaproteobacteria, and Caudovirales are generally under- represented in SSA. Viruses do not transfer to SSA as efficiently as bacteria. The enrichment of mycolic acid-coated Corynebacteriales and lipid-enveloped viruses (inferred from genomic comparisons) suggests that hydrophobic properties increase transport to the sea surface and SSA. Our results identify taxa relevant to atmospheric processes and a framework to further elucidate aerosolization mechanisms influencing microbial and viral transport pathways. 1 Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA. 2 Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA. -
Flavobacterium Gliding Motility: from Protein Secretion to Cell Surface Adhesin Movements
University of Wisconsin Milwaukee UWM Digital Commons Theses and Dissertations August 2019 Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements Joseph Johnston University of Wisconsin-Milwaukee Follow this and additional works at: https://dc.uwm.edu/etd Part of the Biology Commons, Microbiology Commons, and the Molecular Biology Commons Recommended Citation Johnston, Joseph, "Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements" (2019). Theses and Dissertations. 2202. https://dc.uwm.edu/etd/2202 This Dissertation is brought to you for free and open access by UWM Digital Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of UWM Digital Commons. For more information, please contact [email protected]. FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Sciences at The University of Wisconsin-Milwaukee August 2019 ABSTRACT FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston The University of Wisconsin-Milwaukee, 2019 Under the Supervision of Dr. Mark J. McBride Flavobacterium johnsoniae exhibits rapid gliding motility over surfaces. At least twenty genes are involved in this process. Seven of these, gldK, gldL, gldM, gldN, sprA, sprE, and sprT encode proteins of the type IX protein secretion system (T9SS). The T9SS is required for surface localization of the motility adhesins SprB and RemA, and for secretion of the soluble chitinase ChiA. This thesis demonstrates that the gliding motility proteins GldA, GldB, GldD, GldF, GldH, GldI and GldJ are also essential for secretion. -
Extreme Cold Environments: a Suitable Niche for Selection of Novel Psychrotrophic Microbes for Biotechnological Applications
Editorial Adv Biotech & Micro Volume 2 Issue 2 - February 2017 Copyright © All rights are reserved by Ajar Nath Yadav DOI: 10.19080/AIBM.2017.02.555584 Extreme Cold Environments: A Suitable Niche for Selection of Novel Psychrotrophic Microbes for Biotechnological Applications Ajar Nath Yadav1*, Priyanka Verma2, Vinod Kumar1, Shashwati Ghosh Sachan3 and Anil Kumar Saxena4 1Department of Biotechnology, Eternal University, India 2Department of Microbiology, Eternal University, India 3Department of Bio-Engineering, Birla Institute of Technology, India 4ICAR-National Bureau of Agriculturally Important Microorganisms, India Submission: January 27, 2017; Published: February 06, 2017 *Corresponding author: Ajar Nath Yadav, Assistant professor, Department of Biotechnology, Akal College of Agriculture, Eternal University, India, Tel: ; Email: Editorial several reports on whole genome sequences of novel and The microbiomes of cold environments are of particular potential psychrotrophic microbes [26,27]. importance in global ecology since the majority of terrestrial and aquatic ecosystems of our planet are permanently or The novel species of psychrotrophic microbes have been seasonally submitted to cold temperatures. Earth is primarily a isolated worldwide and reported from different domain cold, marine planet with 90% of the ocean’s waters being at 5°C archaea, bacteria and fungi which included members of phylum or lower. Permafrost soils, glaciers, polar sea ice, and snow cover Actinobacteria, Proteobacteria, Bacteroidetes, Basidiomycota, make up 20% of the Earth’s surface environments. Microbial Firmicutes and Euryarchaeota [7-25]. Along with novel species communities under cold habitats have been undergone the of psychrotrophic microbes, some microbial species including physiological adaptations to low temperature and chemical Arthrobacter nicotianae, Brevundimonas terrae, Paenibacillus stress. -
Metagenomics Unveils the Attributes of the Alginolytic Guilds of Sediments from Four Distant Cold Coastal Environments
Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments Marina N Matos1, Mariana Lozada1, Luciano E Anselmino1, Matías A Musumeci1, Bernard Henrissat2,3,4, Janet K Jansson5, Walter P Mac Cormack6,7, JoLynn Carroll8,9, Sara Sjöling10, Leif Lundgren11 and Hebe M Dionisi1* 1Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Chubut, Argentina 2Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France 3INRA, USC 1408 AFMB, F-13288 Marseille, France 4Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia 5Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA 6Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, C1064ABR, Argentina 7Instituto Nanobiotec, CONICET- Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1113AAC, Argentina 8Akvaplan-niva, Fram – High North Research Centre for Climate and the Environment, NO- 9296 Tromsø, Norway 9CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, UiT The Arctic University of Norway, N-9037 Tromsø, Norway 10School of Natural Sciences and Environmental Studies, Södertörn University, 141 89 Huddinge, Sweden 11Stockholm University, SE-106 91 Stockholm, Sweden This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as an ‘Accepted Article’, doi: 10.1111/1462-2920.13433 This article is protected by copyright. All rights reserved. Page 2 of 41 Running title: Alginolytic guilds from cold sediments *Correspondence: Hebe M. -
Discovering Novel Enzymes by Functional Screening of Plurigenomic
Microbiological Research 186–187 (2016) 52–61 Contents lists available at ScienceDirect Microbiological Research j ournal homepage: www.elsevier.com/locate/micres Discovering novel enzymes by functional screening of plurigenomic libraries from alga-associated Flavobacteriia and Gammaproteobacteria a,∗ b a a Marjolaine Martin , Marie Vandermies , Coline Joyeux , Renée Martin , c c a Tristan Barbeyron , Gurvan Michel , Micheline Vandenbol a Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium b Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium c Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, Bretagne, France a r t i c l e i n f o a b s t r a c t Article history: Alga-associated microorganisms, in the context of their numerous interactions with the host and the Received 4 February 2016 complexity of the marine environment, are known to produce diverse hydrolytic enzymes with original Received in revised form 17 March 2016 biochemistry. We recently isolated several macroalgal-polysaccharide-degrading bacteria from the sur- Accepted 22 March 2016 face of the brown alga Ascophyllum nodosum. These active isolates belong to two classes: the Flavobacteriia Available online 24 March 2016 and the Gammaproteobacteria. In the present study, we constructed two “plurigenomic” (with multi- ple bacterial genomes) libraries with the 5 most interesting isolates (regarding their phylogeny and Keywords: their enzymatic activities) of each class (Fv and Gm libraries). Both libraries were screened for diverse Alga-associated microflora hydrolytic activities. -
Agar-Degrading Bacteria Isolated from Antarctic Macroalgae
Folia Microbiol DOI 10.1007/s12223-017-0511-1 Agar-degrading bacteria isolated from Antarctic macroalgae Roxana Alvarado1 & Sergio Leiva1 Received: 17 May 2016 /Accepted: 23 February 2017 # Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2017 Abstract This study describes the taxonomic diversity of Gigartina,andGelidium. The hydrolysis of agar is catalyzed pigmented, agar-degrading bacteria isolated from the surface by agarases which have been classified into three classes of macroalgae collected in King George Island, Antarctica. A based on their mode of action: α-agarase (EC 3.2.1.158), β- total of 30 pigmented, agarolytic bacteria were isolated from agarase (EC 3.2.1.81), and β-porphyranase (EC 3.2.1.–)(Chi the surface of the Antarctic macroalgae Adenocystis et al. 2012). Agarases have potential applications in the food, utricularis, Monostroma hariotii, Iridaea cordata,and cosmetic, and pharmaceutical industries for the production of Pantoneura plocamioides. Based on the 16S rRNA data, the high value-added agaro-oligosaccharides from agar, which agarolytic isolates were affiliated to the genera Algibacter, exhibit various physiological and biological activities (Holdt Arthrobacter, Brachybacterium, Cellulophaga, Citricoccus, and Kraan 2011). Labedella, Microbacterium, Micrococcus, Salinibacterium, Marine bacteria, and in particular those associated with Sanguibacter,andZobellia. Isolates phylogenetically related macroalgae, are a valuable source of novel and exploitable to Cellulophaga algicola showed the highest agarase activity carbohydrate-active enzymes (Michel et al. 2013;Martin in culture supernatants when tested at 4 and 37 °C. This is the et al. 2014). However, only a few studies have explored the first investigation of pigmented agar-degrading bacteria, polysaccharide-degrading activities of Antarctic marine bac- members of microbial communities associated with teria (Tropeano et al. -
The Cell Organization Underlying Structural Colour Is Involved in Flavobacterium IR1 Predation
The ISME Journal (2020) 14:2890–2900 https://doi.org/10.1038/s41396-020-00760-6 ARTICLE The cell organization underlying structural colour is involved in Flavobacterium IR1 predation 1 2 1,3 1 Raditijo Hamidjaja ● Jérémie Capoulade ● Laura Catón ● Colin J. Ingham Received: 29 March 2020 / Revised: 14 August 2020 / Accepted: 24 August 2020 / Published online: 1 September 2020 © The Author(s) 2020. This article is published with open access Abstract Flavobacterium IR1 is a gliding bacterium with a high degree of colonial organization as a 2D photonic crystal, resulting in vivid structural coloration when illuminated. Enterobacter cloacae B12, an unrelated bacterium, was isolated from the brown macroalga Fucus vesiculosus from the same location as IR1. IR1 was found to be a predator of B12. A process of surrounding, infiltration, undercutting and killing of B12 supported improved growth of IR1. A combination of motility and capillarity facilitated the engulfment of B12 colonies by IR1. Predation was independent of illumination. Mutants of IR1 that formed photonic crystals less effectively than the wild type were reduced in predation. Conversely, formation of a photonic crystal was not advantageous in resisting predation by Rhodococcus spp. PIR4. These observations suggest that the 1234567890();,: 1234567890();,: organization required to create structural colour has a biological function (facilitating predation) but one that is not directly related to the photonic properties of the colony. This work is the first experimental evidence supporting a role for this widespread type of cell organization in the Flavobacteriia. Introduction to highly repeated arrays of cells which can assemble rapidly to form a 2D photonic crystal (2DPC) [1], a form of Flavobacterium IR1 is a gliding bacterium that can spread structural colour (SC), which is distinct in mechanism from over hydrated surfaces [1].