DOCSLIB.ORG

Vibrio Cholerae Crts Site and Its Role on the Coordinated Replication of the Two Chromosomes Francisco De Lemos Martins

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Vibrio Cholerae Crts Site and Its Role on the Coordinated Replication of the Two Chromosomes Francisco De Lemos Martins Decrypting the Vibrio cholerae crtS site and its role on the coordinated replication of the two chromosomes Francisco de Lemos Martins To cite this version: Francisco de Lemos Martins. Decrypting the Vibrio cholerae crtS site and its role on the coordi- nated replication of the two chromosomes. Genetics. Sorbonne Université, 2018. English. NNT : 2018SORUS126. tel-02926056 HAL Id: tel-02926056 https://tel.archives-ouvertes.fr/tel-02926056 Submitted on 31 Aug 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Sorbonne Université Complexité du Vivant Institut Pasteur – Unité Plasticité du Génome Bactérien Decrypting the Vibrio cholerae crtS site and its role on the coordinated replication of the two chromosomes Par Francisco de Lemos Martins Thèse de doctorat de Microbiologie et Génétique Dirigée par Didier Mazel Présentée et soutenue publiquement le 26 juin 2018 Devant un jury composé de : Pr. Guennadi SEZONOV Professeur Président du jury Pr. Justine COLLIER Directeur de Recherche Rapporteur Dr. Franck PASTA Enseignant/Chercheur Rapporteur Dr. Christophe POSSOZ Chargé de Recherche Examinateur Dr. Stéphane DUIGOU Chargé de Recherche Examinateur Pr. Didier MAZEL Professeur Directeur de thèse Dr. Marie-Eve VAL Chargé de Recherche Co-Encadrant de thèse ABSTRACT Bacterial genomes are mainly composed of two types of replicons: chromosomes, which are essential, and plasmids. Although most bacteria have only one chromosome, bacteria with secondary chromosomes have arisen independently in several taxa and represent approximately 10% of all bacterial species. Secondary chromosomes originate from plasmids and possess plasmid-type replication systems. While chromosomes replicate once and during a defined period of the cell cycle, plasmids generally replicate randomly. Vibrio cholerae has its genome divided in two chromosomes (Chr1 and Chr2) that use distinct initiators for replication. Chr1 replication depends on the ubiquitous initiator DnaA, while Chr2 replication is initiated by a Vibrio specific factor, RctB. Despite its plasmid origins, Chr2 replication is tightly controlled and occurs once per cell cycle. Both chromosomes communicate with each other to coordinate their replication through an RctB-binding locus on Chr1, called crtS. We have shown that crtS replication is crucial to trigger Chr2 replication initiation. However, the molecular mechanism by which crtS controls the initiation of Chr2 replication was still obscure. Here we combined in vivo and in vitro approaches to shed light on this question. We have shown that crtS activity is driven by RctB binding in a methylation-independent manner. Furthermore, functional analysis of crtS mutants suggests that its single stranded form may adopt a hairpin conformation upon passage of the replication fork, which somehow activates Chr2 replication. This mechanism appears to be an effective way to integrate the Chr2 replication in the cell cycle. ACKNOWLEDGEMENTS This thesis reflects the support of many people who influenced my work in different ways and to whom I would like to thank. First, I would like to thank the jury members for having accepted to judge this thesis, either as reviewers, Dr. Justine Collier and Dr. Franck Pasta, or as examiners, Dr. Christophe Possoz and Dr. Stéphane Duigou. I would also like to express my gratitude to Prof. Guennadi Sezonov for having accepted to be the president of the jury. I am very grateful to my supervisor Didier Mazel who kindly accepted me in his lab and for the trust he has put on me to conduct this project. Thank you for all your support throughout these years. Your constant optimism and good mood certainly helped me to be more motivated during this thesis. I would like to express my gratitude to Marie-Eve Val, for being an extraordinary supervisor and for the continuous support during my thesis. Thank you for your patience, your motivation and for your precious guidance. Thank you for sharing your wisdom and for allowing me to learn with your experience. Without your supervision and constant help this thesis would not have been possible. I want to thank all the present and previous lab members with whom I had the opportunity to work with. Aleks, Alfonso, Céline, Christophe, Claire, Evelyne, Jakub, José, Julia, Magaly, Rocio, Sebastian and Zeynep: thank you for your helpful advice and for having always created a good environment in the lab. It was a great pleasure to work with you! Jason, thank you for having guided me during my first days in the lab when I was starting the PhD adventure. Thank you Florian for all the help and support, and for your precious contribution to this work. And also for the famous “pause cigarette”! Veronica, thank you for your true friendship and for all the great moments that we spent together during this journey. I will never forget how snapchat made our days more joyful! Even if I kept on escaping from the Portuguese lunches, I would like to thank the Portuguese community in Pasteur, especially Sofia, Jorge, Marisa, Carolina and André! Obrigado por me fazerem falar português de vez em quando e de não me fazerem esquecer a “língua de Camões”! I would like to thank the PPU program and all the people involved for the effort you put in the organization of this great program for international PhD students. I also would like to thank my PPU fellows for the great moments we spent together, especially during the retreats. I could not have survived these last three years and half without the support of my friends, even if some are a bit far. Thank you Carlota, Catarina S., Joana F., Joana M., Mafalda, Rafael, Sofia and Vera. Thank you for your visits, your friendship and for being always by my side since our university times! I also would like to thank the friends I made since my arrival in France, especially Maria-Vittoria and Benedetta. This adventure wouldn’t have been the same without you! I am profoundly grateful to Marco for all the support and immense patience during the last months. I know it has been a though journey and I am very thankful to have you by my side. Thank you for your constant motivating words, always encouraging me to move forward. A very special acknowledgment to my parents, my brother and my sister-in-law for always supporting my decisions and for being there for me whenever I needed. Thank you for your regular visits and for making the physical distance between us feel a little bit shorter than what it actually is. Muito obrigado pelo vosso apoio incondicional e por estarem sempre disponíveis. Obrigado pelas vossas visitas frequentes e por me fazerem sentir a distância um bocadinho mais curta do que aquela que na realidade nos separa. TABLE OF CONTENTS INTRODUCTION .......................................................................................................................... 9 I. Bacterial genome organization ............................................................................................... 9 1.1. Chromosomes ........................................................................................................................ 10 1.2. Plasmids and Megaplasmids .................................................................................................. 10 1.3. Chromids or secondary chromosomes ................................................................................... 11 1.4. Phylogenetic Distribution of Multipartite Genomes .............................................................. 12 1.5. Mechanisms of Chromid Formation ....................................................................................... 14 1.5.1. The Schism Hypothesis .................................................................................................... 14 1.5.2. The Plasmid Hypothesis................................................................................................... 15 1.5.3. Megaplasmid Domestication ........................................................................................... 16 II. Replication of bacterial replicons ........................................................................................ 19 2.1. Chromosome replication : the E. coli model .......................................................................... 19 2.1.1. Initiation of chromosome replication .............................................................................. 19 2.1.2. Helicase loading in bacteria/Replisome formation ......................................................... 22 2.1.3. Chromosome Replication Termination ........................................................................... 22 2.1.3.1. E.coli Tus-Ter system ................................................................................................ 23 2.1.3.2. B. subtilis RTP-Ter system ......................................................................................... 23 2.1.4. Regulation of chromosome replication ........................................................................... 23 2.1.4.1. Regulation at the origin sequence in E. coli ............................................................
Load more

Recommended publications
  • Burkholderia Cenocepacia Integrates Cis-2-Dodecenoic Acid and Cyclic Dimeric Guanosine Monophosphate Signals to Control Virulence
    Burkholderia cenocepacia integrates cis-2-dodecenoic acid and cyclic dimeric guanosine monophosphate signals to control virulence Chunxi Yanga,b,c,d,1, Chaoyu Cuia,b,c,1, Qiumian Yea,b, Jinhong Kane, Shuna Fua,b, Shihao Songa,b, Yutong Huanga,b, Fei Hec, Lian-Hui Zhanga,c, Yantao Jiaf, Yong-Gui Gaod, Caroline S. Harwoodb,g,2, and Yinyue Denga,b,c,2 aState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; bGuangdong Innovative Research Team of Sociomicrobiology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; cIntegrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; dSchool of Biological Sciences, Nanyang Technological University, Singapore 637551; eCenter for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; fState Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; and gDepartment of Microbiology, University of Washington, Seattle, WA 98195 Contributed by Caroline S. Harwood, October 30, 2017 (sent for review June 1, 2017; reviewed by Maxwell J. Dow and Tim Tolker-Nielsen) Quorum sensing (QS) signals are used by bacteria to regulate N-octanoyl homoserine lactone (C8-HSL). The two QS systems biological functions in response to cell population densities. Cyclic have both distinct and overlapping effects on gene expression diguanosine monophosphate (c-di-GMP) regulates cell functions in (16, 17). response to diverse environmental chemical and physical signals One of the ways in which QS systems can act is by controlling that bacteria perceive. In Burkholderia cenocepacia, the QS signal levels of intracellular cyclic diguanosine monophosphate (c-di-GMP) receptor RpfR degrades intracellular c-di-GMP when it senses the in bacteria (18–21).
    [Show full text]
  • Cholera Transmission: the Host, Pathogen and Bacteriophage Dynamic
    REVIEWS Cholera transmission: the host, pathogen and bacteriophage dynamic Eric J. Nelson*, Jason B. Harris‡§, J. Glenn Morris Jr||, Stephen B. Calderwood‡§ and Andrew Camilli* Abstract | Zimbabwe offers the most recent example of the tragedy that befalls a country and its people when cholera strikes. The 2008–2009 outbreak rapidly spread across every province and brought rates of mortality similar to those witnessed as a consequence of cholera infections a hundred years ago. In this Review we highlight the advances that will help to unravel how interactions between the host, the bacterial pathogen and the lytic bacteriophage might propel and quench cholera outbreaks in endemic settings and in emergent epidemic regions such as Zimbabwe. 15 O antigen Diarrhoeal diseases, including cholera, are the leading progenitor O1 El Tor strain . Although the O139 sero- The outermost, repeating cause of morbidity and the second most common cause group caused devastating outbreaks in the 1990s, the El oligosaccharide portion of LPS, of death among children under 5 years of age globally1,2. Tor strain remains the dominant strain globally11,16,17. which makes up the outer It is difficult to gauge the exact morbidity and mortality An extensive body of literature describes the patho- leaflet of the outer membrane of Gram-negative bacteria. of cholera because the surveillance systems in many physiology of cholera. In brief, pathogenic strains har- developing countries are rudimentary, and many coun- bour key virulence factors that include cholera toxin18 Cholera toxin tries are hesitant to report cholera cases to the WHO and toxin co-regulated pilus (TCP)19,20, a self-binding A protein toxin produced by because of the potential negative economic impact pilus that tethers bacterial cells together21, possibly V.
    [Show full text]
  • Downloaded 13 April 2017); Using Diamond
    bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 3 4 5 Re-evaluating the salty divide: phylogenetic specificity of 6 transitions between marine and freshwater systems 7 8 9 10 Sara F. Pavera, Daniel J. Muratorea, Ryan J. Newtonb, Maureen L. Colemana# 11 a 12 Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA 13 b School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA 14 15 Running title: Marine-freshwater phylogenetic specificity 16 17 #Address correspondence to Maureen Coleman, [email protected] 18 bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 Abstract 20 Marine and freshwater microbial communities are phylogenetically distinct and transitions 21 between habitat types are thought to be infrequent. We compared the phylogenetic diversity of 22 marine and freshwater microorganisms and identified specific lineages exhibiting notably high or 23 low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA 24 gene tag-sequencing datasets. As expected, marine and freshwater microbial communities 25 differed in the relative abundance of major phyla and contained habitat-specific lineages; at the 26 same time, however, many shared taxa were observed in both environments. 27 Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between 28 marine and freshwater sample pairs.
    [Show full text]
  • Inverse Regulation of Vibrio Cholerae Biofilm Dispersal by Polyamine Signals Andrew a Bridges1,2, Bonnie L Bassler1,2*
    RESEARCH ARTICLE Inverse regulation of Vibrio cholerae biofilm dispersal by polyamine signals Andrew A Bridges1,2, Bonnie L Bassler1,2* 1Department of Molecular Biology, Princeton University, Princeton, United States; 2The Howard Hughes Medical Institute, Chevy Chase, United States Abstract The global pathogen Vibrio cholerae undergoes cycles of biofilm formation and dispersal in the environment and the human host. Little is understood about biofilm dispersal. Here, we show that MbaA, a periplasmic polyamine sensor, and PotD1, a polyamine importer, regulate V. cholerae biofilm dispersal. Spermidine, a commonly produced polyamine, drives V. cholerae dispersal, whereas norspermidine, an uncommon polyamine produced by vibrios, inhibits dispersal. Spermidine and norspermidine differ by one methylene group. Both polyamines control dispersal via MbaA detection in the periplasm and subsequent signal relay. Our results suggest that dispersal fails in the absence of PotD1 because endogenously produced norspermidine is not reimported, periplasmic norspermidine accumulates, and it stimulates MbaA signaling. These results suggest that V. cholerae uses MbaA to monitor environmental polyamines, blends of which potentially provide information about numbers of ‘self’ and ‘other’. This information is used to dictate whether or not to disperse from biofilms. Introduction Bacteria frequently colonize environmental habitats and infection sites by forming surface-attached multicellular communities called biofilms. Participating in the biofilm lifestyle allows bacteria to col- lectively acquire nutrients and resist threats (Flemming et al., 2016). By contrast, the individual free- *For correspondence: swimming state allows bacteria to roam. The global pathogen Vibrio cholerae undergoes repeated [email protected] rounds of clonal biofilm formation and disassembly, and both biofilm formation and biofilm exit are central to disease transmission as V.
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • Impact of Helicobacter Pylori Eradication Therapy on Gastric Microbiome
    Impact of Helicobacter Pylori Eradication Therapy on Gastric Microbiome Liqi Mao The First Aliated Hospital of Zhejiang Chinese Medical University https://orcid.org/0000-0002-5972- 4746 Yanlin Zhou The First Aliated Hospital of Zhejiang Chinese Medical University Shuangshuang Wang The First Aliated Hospital of Zhejiang Chinese Medical University Lin Chen The First Aliated Hospital of Zhejiang Chinese Medical University Yue Hu The First Aliated Hospital of Zhejiang Chinese Medical University Leimin Yu The First Aliated Hospital of Zhejiang Chinese Medical University Jingming Xu The First Aliated Hospital of Zhejiang Chinese Medical University Bin Lyu ( [email protected] ) First Aliated Hospital of Zhejiang Chinese Medical University https://orcid.org/0000-0002-6247-571X Research Keywords: 16S rRNA gene sequencing, Helicobacter pylori, Eradication therapy, Gastric microora, Atrophic gastritis Posted Date: April 29th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-455395/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 Impact of Helicobacter pylori eradication therapy on gastric microbiome 2 Liqi Mao 1,#, Yanlin Zhou 1,#, Shuangshuang Wang1,2, Lin Chen1, Yue Hu 1, Leimin Yu1,3, 3 Jingming Xu1, Bin Lyu1,* 4 1Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical 5 University, Hangzhou, China 6 2Department of Gastroenterology, Taizhou Hospital of Zhejiang Province affiliated to 7 Wenzhou Medical University, Taizhou, China 8 3Department of Gastroenterology, Guangxing Hospital Affiliated to Zhejiang Chinese 9 Medical University, Hangzhou, China 10 #Liqi Mao and Yanlin Zhou contributed equally. 11 *Bin Lyu is the corresponding author, Email: [email protected].
    [Show full text]
  • Yu-Chen Ling and John W. Moreau
    Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig.
    [Show full text]
  • Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment
    antibiotics Article Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment Alicia Sorgen 1, James Johnson 2, Kevin Lambirth 2, Sandra M. Clinton 3 , Molly Redmond 1 , Anthony Fodor 2 and Cynthia Gibas 2,* 1 Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (A.S.); [email protected] (M.R.) 2 Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (J.J.); [email protected] (K.L.); [email protected] (A.F.) 3 Department of Geography & Earth Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-704-687-8378 Abstract: Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify Citation: Sorgen, A.; Johnson, J.; phenotypically resistant cultivable portions of these bacterial communities and characterized the Lambirth, K.; Clinton,
    [Show full text]
  • Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
    RESEARCH ARTICLE Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes Rachel E. Diner,a,b,c Drishti Kaul,c Ariel Rabines,a,c Hong Zheng,c Joshua A. Steele,d John F. Griffith,d Andrew E. Allena,c aScripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA bDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA cMicrobial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California, USA dSouthern California Coastal Water Research Project, Costa Mesa, California, USA ABSTRACT Interactions between vibrio bacteria and the planktonic community impact marine ecology and human health. Many coastal Vibrio spp. can infect humans, represent- ing a growing threat linked to increasing seawater temperatures. Interactions with eukaryo- tic organisms may provide attachment substrate and critical nutrients that facilitate the per- sistence, diversification, and spread of pathogenic Vibrio spp. However, vibrio interactions with planktonic organisms in an environmental context are poorly understood. We quanti- fied the pathogenic Vibrio species V. cholerae, V. parahaemolyticus,andV. vulnificus monthly for 1 year at five sites and observed high abundances, particularly during summer months, with species-specific temperature and salinity distributions. Using metabarcoding, we estab- lished a detailed profile of both prokaryotic and eukaryotic coastal microbial communities. We found that pathogenic Vibrio species were frequently associated with distinct eukaryo- tic amplicon sequence variants (ASVs), including diatoms and copepods. Shared environ- mental conditions, such as high temperatures and low salinities, were associated with both high concentrations of pathogenic vibrios and potential environmental reservoirs, which may influence vibrio infection risks linked to climate change and should be incorporated into predictive ecological models and experimental laboratory systems.
    [Show full text]
  • Wedding Higher Taxonomic Ranks with Metabolic Signatures Coded in Prokaryotic Genomes
    Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes Gregorio Iraola*, Hugo Naya* Corresponding authors: E-mail: [email protected], [email protected] This PDF file includes: Supplementary Table 1 Supplementary Figures 1 to 4 Supplementary Methods SUPPLEMENTARY TABLES Supplementary Tab. 1 Supplementary Tab. 1. Full prediction for the set of 108 external genomes used as test. genome domain phylum class order family genus prediction alphaproteobacterium_LFTY0 Bacteria Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae Unknown candidatus_nasuia_deltocephalinicola_PUNC_CP013211 Bacteria Proteobacteria Gammaproteobacteria Unknown Unknown Unknown candidatus_sulcia_muelleri_PUNC_CP013212 Bacteria Bacteroidetes Flavobacteriia Flavobacteriales NA Candidatus Sulcia deinococcus_grandis_ATCC43672_BCMS0 Bacteria Deinococcus-Thermus Deinococci Deinococcales Deinococcaceae Deinococcus devosia_sp_H5989_CP011300 Bacteria Proteobacteria Unknown Unknown Unknown Unknown micromonospora_RV43_LEKG0 Bacteria Actinobacteria Actinobacteria Micromonosporales Micromonosporaceae Micromonospora nitrosomonas_communis_Nm2_CP011451 Bacteria Proteobacteria Betaproteobacteria Nitrosomonadales Nitrosomonadaceae Unknown nocardia_seriolae_U1_BBYQ0 Bacteria Actinobacteria Actinobacteria Corynebacteriales Nocardiaceae Nocardia nocardiopsis_RV163_LEKI01 Bacteria Actinobacteria Actinobacteria Streptosporangiales Nocardiopsaceae Nocardiopsis oscillatoriales_cyanobacterium_MTP1_LNAA0 Bacteria Cyanobacteria NA Oscillatoriales
    [Show full text]
  • Vibrio: Myths Vs. Facts “Flesh-Eating Bacteria” Is a Phrase Often At- Weakened Immune Systems Are at Higher Risk Inside This Issue
    Public Health Information for Community Partners 5150 NW Milner Dr. prime Port St. Lucie, FL 34983 EPIsodes 15 August 2015 Phone (772) 462‐ 3800 www.stluciecountyhealth.com/ Vibrio: Myths vs. Facts “Flesh-eating bacteria” is a phrase often at- weakened immune systems are at higher risk Inside this issue... tached to infections associated with the group for these type of infections as well. Called a of bacteria called Vibrios. This phrase is also “necrotizing skin infection,” this is a rare, very Vibrio: Myths vs. often followed by the warning that these bacte- severe infection that can destroy muscles, skin Facts 1 ria have been found in local waters and that and surrounding tissues. SLC Reportable someone died after getting infected. Many different bacteria can cause necrotizing Diseases While “flesh eating bacteria” is a media fa- fasciitis. Streptococcus (group A Strep) is the Incidence Report 2 vorite, it is misleading, inaccurate and creates most common cause. Others include: Staph anxiety for many people. The presence of Vib- aureus (found on most people’s skin), E. coli, rios in nature does not mean that anyone who and Clostridium, to name a few. goes swimming or fishing risks a skin dissolv- “NO VIBRIO” TIPS ing bacterial infection. Continue to enjoy your water and beach activi- Fact is, Vibrios are a group of free-living bac- ties using the following prevention measures: teria found in coastal waters worldwide that Additional Vibrio Vulnificus If you have a weakened immune system, liv- reproduce rapidly in warmer, brackish or low information can be found at: er disease or other chronic condition, avoid http://www.floridahealth.gov/ salt waters.
    [Show full text]
  • Phylogenetically Conserved Resource Partitioning in the Coastal Microbial Loop
    OPEN The ISME Journal (2017) 11, 2781–2792 www.nature.com/ismej ORIGINAL ARTICLE Phylogenetically conserved resource partitioning in the coastal microbial loop Samuel Bryson1, Zhou Li2,3, Francisco Chavez4, Peter K Weber5, Jennifer Pett-Ridge5, Robert L Hettich2,3, Chongle Pan2,3, Xavier Mayali5 and Ryan S Mueller1 1Department of Microbiology, Oregon State University, Corvallis, OR, USA; 2Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, USA; 3Oak Ridge National Laboratory, Oak Ridge, TN, USA; 4Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA and 5Lawrence Livermore National Laboratory, Livermore, CA, USA Resource availability influences marine microbial community structure, suggesting that population- specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive.
    [Show full text]