DOCSLIB.ORG

Resistance to Pear Decline Phytoplasma and Its Relationship to Pathogen

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Resistance to Pear Decline Phytoplasma and Its Relationship to Pathogen Resistance to pear decline phytoplasma and its relationship to pathogen overwintering, host response and foliar symptoms by Mina Kaviani A Thesis Presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Plant Agriculture Guelph, Ontario, Canada © Mina Kaviani, August, 2014 Abstract Resistance to pear decline phytoplasma and its relationship to pathogen overwintering, host response and foliar symptoms Mina Kaviani Co-advisors: University of Guelph, 2014 Dr. D. M. Hunter Dr. P. H. Goodwin Pear Decline (PD) phytoplasma populations were measured using quantitative real-time PCR over a year in non-symptomatic pear trees (HW620 as scion) on the rootstocks, OH×F87 (PD resistant), OH×F69 (PD susceptible) and Bartlett (PD susceptible), growing in the Niagara region (Ontario, Canada). Seasonal patterns of PD populations were not greatly altered by the rootstock. Maximum populations occurred during late summer for leaves and shoots, and minimums during mid-winter for shoots and early spring for leaves, whereas maximum populations in roots were in mid-winter and minimums in mid-spring. PD populations for each month were typically less in leaves than in shoots, but both were much less than in roots. Regardless of tissue type, PD populations were lowest with OH×F87, then higher with OH×F69 and highest with Bartlett rootstock indicating that rootstock resistance affects PD populations in scion tissues. PD phytoplasma populations and expression patterns of six pear genes were also compared between leaves, shoots and roots of non- infected and PD-infected pear trees showing symptoms of leaf curling (selection 9328-1) or leaf reddening (selection 8824-1). The only significant differences in PD populations were higher numbers in roots of selection 9328-1 than 8824-1. More genes had significantly higher expression in PD-infected than non-infected tissues for selection 8824-1 than 9328-1 indicating stronger host responses. A comparison of PD-infected selection 8824-1 to 9328-1 showed greater up-regulation of genes in selection 8824-1 for sucrose synthase in leaves, acid invertase in leaves and roots, alcohol dehydrogenase in shoots, chitinase in all tissues, and phloem protein in roots, whereas greater up-regulation in PD-infected selection 9328-1 than 8824-1 was observed only in shoots for sucrose synthase, acid invertase and phenylalanine ammonia-lyase. Up-regulation of sucrose synthase and acid invertase could be associated to localized changes in sugars, while up-regulation of alcohol dehydrogenase, chitinase class III, phenylalanine ammonia-lyase and phloem protein2 could be part of triggered immunity. The results indicate that leaf reddening may be due to greater triggered immunity in selection 8824-1 resulting in an accumulation of anthocyanins, while leaf curling in selection 9328-1 may be due to water stress because of more dysfunctional phloem. Acknowledgments I would like to express my gratitude to my advisor, Dr. David Hunter, for providing me with the opportunity to pursue my research in plant agriculture. I benefited from his vast knowledge in pear breeding and horticulture, which enriched my experience in working on pears. I was fortunate to have Dr. Goodwin as my advisor, whose knowledge of plant pathology amazed me in several ways and his analytical knowledge helped me considerably in writing my thesis. I would like to thank the other members of my committee: Dr. Annette Nassuth for the assistance she provided in part of my lab work during my first part of study, sharing her expertise in molecular biology methods and teaching me the real meaning of organization in a lab; and Dr. Larry Erickson for serving on my advisory committee. I want to thank all the kind people I met at the Vineland Station campus of the University of Guelph and Agriculture and Agri-Food Canada (AAFC). My thanks go to Cheryl Collucci for welcoming me into the laboratory and teaching me many molecular techniques, and to Darlene Nesbitt whom I would never forget for her endless support and love during my lab work at Vineland Station in Dr. Hunter's lab. She has been a source of love and energy ever since. I must also acknowledge Dr. Peter Pauls for departmental support in covering my tuition fees. Appreciation also goes out to Jean Wolting who provided best advice to make my graduate program less stressful. Thanks also goes out to Dr. Chrystel Olivier and Dr. Istvan Rajcan, who kindly agreed to be my external and internal examiners, and their feedback in the final stages of my degree was invaluable. I would like to thank my parents and siblings for the support they provided me through my entire life and for their encouraging presence in my daily life throughout my graduate studies, despite the geographical distance. Last, but by no means least, I acknowledge my partner in life and my best friend, Mostafa, without whose love, and patience, I would not have finished this thesis. III Table of Contents Acknowledgments..........................................................................................................................III Table of Contents .......................................................................................................................... IV List of Tables ............................................................................................................................... VII List of Figures ............................................................................................................................. VIII List of Abbreviations ................................................................................................................... XII Chapter 1 ......................................................................................................................................... 1 Literature Review............................................................................................................................ 1 1.1. Introduction .......................................................................................................................... 1 1.2. Phytoplasma disease and their economic importance.......................................................... 2 1.3. Symptoms and spread of phytoplasma disease .................................................................... 3 1.4. 16SrX: Apple Proliferation group........................................................................................ 5 1.4.1. Pear Decline, Candidatus Phytoplasma pyri.................................................................... 6 1.4.2. PD resistance .................................................................................................................... 8 1.5. Phytoplasma detection and identification ............................................................................ 9 1.5.1. Electron microscopy and DAPI staining ........................................................................ 11 1.5.2. Dot-blot hybridization .................................................................................................... 12 1.5.3. Polymerase Chain Reaction ........................................................................................... 13 1.5.4. Apple proliferation (AP)-specific PCR .......................................................................... 14 1.5.5. Restriction Fragment Length Polymorphisms (RFLP) .................................................. 16 1.5.6. Real-Time PCR .............................................................................................................. 17 1.6. Colonization of woody plants by phytoplasmas ................................................................ 18 1.7. Phytoplasma genes and genomes ....................................................................................... 19 1.8. Phytoplasma pathogenicity and virulence ......................................................................... 22 1.9. Phytoplasma - plant interactions ........................................................................................ 24 1.9.1. Phytoplasma effects on plant development .................................................................... 24 1.9.2. Phytoplasma effects on photosynthesis and sugar metabolism...................................... 25 1.9.3. Phytoplasma effects on plant secondary metabolites ..................................................... 27 IV 1.9.4. Phytoplasma effects on plant gene expression ............................................................... 28 1.10. Research goals...................................................................................................................... 33 1.11. Hypothesis and objectives.................................................................................................... 34 1.11.1. Hypothesis......................................................................................................................... 34 1.11.2. Objectives.......................................................................................................................... 34 Chapter 2 ....................................................................................................................................... 41 Pear rootstock effects on seasonal colonization pattern of pear decline phytoplasma ................. 41 2.1. Introduction ............................................................................................................................ 41 2.2.
Load more

Recommended publications
  • Bacterial Communities of the Upper Respiratory Tract of Turkeys
    www.nature.com/scientificreports OPEN Bacterial communities of the upper respiratory tract of turkeys Olimpia Kursa1*, Grzegorz Tomczyk1, Anna Sawicka‑Durkalec1, Aleksandra Giza2 & Magdalena Słomiany‑Szwarc2 The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplifcation of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identifed in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Diferences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identifed, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey focks. Next-generation sequencing has resulted in a marked increase in culture-independent studies characterizing the microbiome of humans and animals1–6. Much of these works have been focused on the gut microbiome of humans and other production animals 7–11.
    [Show full text]
  • Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
    ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
    [Show full text]
  • MIB–MIP Is a Mycoplasma System That Captures and Cleaves Immunoglobulin G
    MIB–MIP is a mycoplasma system that captures and cleaves immunoglobulin G Yonathan Arfia,b,1, Laetitia Minderc,d, Carmelo Di Primoe,f,g, Aline Le Royh,i,j, Christine Ebelh,i,j, Laurent Coquetk, Stephane Claveroll, Sanjay Vasheem, Joerg Joresn,o, Alain Blancharda,b, and Pascal Sirand-Pugneta,b aINRA (Institut National de la Recherche Agronomique), UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; bUniversity of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; cInstitut Européen de Chimie et Biologie, UMS 3033, University of Bordeaux, 33607 Pessac, France; dInstitut Bergonié, SIRIC BRIO, 33076 Bordeaux, France; eINSERM U1212, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; fCNRS UMR 5320, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; gInstitut Européen de Chimie et Biologie, University of Bordeaux, 33607 Pessac, France; hInstitut de Biologie Structurale, University of Grenoble Alpes, F-38044 Grenoble, France; iCNRS, Institut de Biologie Structurale, F-38044 Grenoble, France; jCEA, Institut de Biologie Structurale, F-38044 Grenoble, France; kCNRS UMR 6270, Plateforme PISSARO, Institute for Research and Innovation in Biomedicine - Normandie Rouen, Normandie Université, F-76821 Mont-Saint-Aignan, France; lProteome Platform, Functional Genomic Center of Bordeaux, University of Bordeaux, F-33076 Bordeaux Cedex, France; mJ. Craig Venter Institute, Rockville, MD 20850; nInternational Livestock Research Institute, 00100 Nairobi, Kenya; and oInstitute of Veterinary Bacteriology, University of Bern, CH-3001 Bern, Switzerland Edited by Roy Curtiss III, University of Florida, Gainesville, FL, and approved March 30, 2016 (received for review January 12, 2016) Mycoplasmas are “minimal” bacteria able to infect humans, wildlife, introduced into naive herds (8).
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Data Sheet on Spiroplasma Citri
    Prepared by CABI and EPPO for the EU under Contract 90/399003 Data Sheets on Quarantine Pests Spiroplasma citri The vectors of Spiroplasma citri are individually included in EU Directive 77/93. Since their importance only arises in relation to S. citri, they are covered in this data sheet. IDENTITY • Spiroplasma citri Name: Spiroplasma citri Saglio et al. Taxonomic position: Bacteria: Tenericutes: Mollicutes Common names: Stubborn, little leaf (English) Stubborn (French) Bayer computer code: SPIRCI EU Annex designation: II/A2 • Circulifer tenellus Name: Circulifer tenellus (Baker) Synonyms: Neoaliturus tenellus (Baker) Eutettix tenellus Baker Taxonomic position: Insecta: Hemiptera: Homoptera: Cicadellidae Common names: Beet leafhopper (English) Cicadelle de la betterave (French) Saltahojas de la remolacha (Spanish) Notes on taxonomy and nomenclature: Oman (1970) argues for the retention of Circulifer and Neoaliturus as separate genera; in his concept both tenellus and haematoceps are placed in Circulifer. Nast (1972) treats the two genera as Neoaliturus notwithstanding Oman's (1970) arguments for the retention of the two genera. He includes 17 species in the Palaearctic region of which 14 are recorded from the Mediterranean Basin. The two species, tenellus and haematoceps, are both included in Circulifer by della Giustina (1989), who reports that tenellus is confirmed in Corsica. Bayer computer code: CIRCTE EU Annex designation: II/A2 • Neoaliturus haematoceps Name: Neoaliturus haematoceps (Mulsant & Rey) Synonyms: Circulifer haematoceps (Mulsant & Rey) Jassus haematoceps Mulsant & Rey Taxonomic position: Insecta: Hemiptera: Homoptera: Cicadellidae Bayer computer code: NEOAHA EU Annex designation: II/A2 (under the name Circulifer haematoceps) HOSTS • Spiroplasma citri The principal economic hosts of S. citri are susceptible Citrus spp.
    [Show full text]
  • Downloaded from Genome Website
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.18.388454; this version posted November 19, 2020. 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 Characterization of the first cultured free-living representative of 2 Candidatus Izimaplasma uncovers its unique biology 3 Rikuan Zheng1,2,3,4, Rui Liu1,2,4, Yeqi Shan1,2,3,4, Ruining Cai1,2,3,4, Ge Liu1,2,4, Chaomin Sun1,2,4* 1 4 CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea 5 Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China 2 6 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory 7 for Marine Science and Technology, Qingdao, China 3 8 College of Earth Science, University of Chinese Academy of Sciences, Beijing, 9 China 10 4Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China 11 12 * Corresponding author 13 Chaomin Sun Tel.: +86 532 82898857; fax: +86 532 82898857. 14 E-mail address: [email protected] 15 16 17 Key words: Candidatus Izimaplasma, uncultivation, biogeochemical cycling, 18 extracellular DNA, in situ, deep sea 19 Running title: Characterization of the first cultured Izimaplasma 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.18.388454; this version posted November 19, 2020. 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. 22 Abstract 23 Candidatus Izimaplasma, an intermediate in the reductive evolution from Firmicutes 24 to Mollicutes, was proposed to represent a novel class of free-living wall-less bacteria 25 within the phylum Tenericutes found in deep-sea methane seeps.
    [Show full text]
  • Lists of Names of Prokaryotic Candidatus Taxa
    NOTIFICATION LIST: CANDIDATUS LIST NO. 1 Oren et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.003789 Lists of names of prokaryotic Candidatus taxa Aharon Oren1,*, George M. Garrity2,3, Charles T. Parker3, Maria Chuvochina4 and Martha E. Trujillo5 Abstract We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, pro- posed between the mid- 1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evo- lutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current propos- als to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes. Introduction of the category called Candidatus was first pro- morphology, basis of assignment as Candidatus, habitat, posed by Murray and Schleifer in 1994 [1]. The provisional metabolism and more. However, no such lists have yet been status Candidatus was intended for putative taxa of any rank published in the journal. that could not be described in sufficient details to warrant Currently, the nomenclature of Candidatus taxa is not covered establishment of a novel taxon, usually because of the absence by the rules of the Prokaryotic Code.
    [Show full text]
  • Mental Figure 1 Color Key a -2 0 2 B Z-Score 100%
    Supplemental Figure 1 Color Key A -2 0 2 B z-score 100% 75% 50% 25% 0% KC pan 1 WT pan 3 WT KC pan 3 WT pan 2 WT pan 1 WT KC pan 2 C Color Key D a: Brevibacterium f: Chlamydiales b: Brevibacteriaceae g: Chlamydiia -3 0 3 z-score c: Sphingobacteriaceae h: Chlamydiae d: Sphingobacteriales i: Mogibacterium e: Sphingobacteriia j: Oscillospira k: Methylobacteriaceae NML Control Microb.-entrained MΦ PDA PDA Patient Population Control Microb.-entrained MΦ + Myd88i E F Ctrl Abx 350 * 300 250 200 150 40X 100 Tumor weight (mg) 50 0 x Ctrl Ab Supplemental Figure 2 A KC WT B ** * Actinobacteria * ** Bacteroidetes Cyanobacteria Deferribacteres * Firmicutes Proteobacteria % Relative abundance TM7 Others Time(wks) 3 9 13 16 20 24 28 32 36 3 9 13 16 20 24 28 32 36 Alpha Diversity Measure C E 60 KC WT 40 20 B. pseudolongum B. animalis 60 5 KC WT 0 B. adolescentis 40% Rel. abundance 3 9 13 16 20 24 28 32 36 3 9 13 16 20 24 28 32 36 20 Age (weeks) B. pseudolongum B. animalis 5 0 B. adolescentis % Rel. abundance 3 9 13 16 20 24 28 32 36 3 9 13 16 20 24 28 32 36 F Age (weeks) Week 3 Week 9 Week 13 p=0.678 p=0.02 p=0.385 Time(wks) 3 9 24 20 13 16 D 28 32 36 Week 13 KC WT Firmicutes; Ruminococcus Firmicutes; Dehalobacterium Alpha Diversity Measure Firmicutes; Oscillospira Bacteroidates; Odoribacter Axis.2 [12.7%] Actinobacteria; Bifidobacterium Axis.2 [23.8%] Axis.2 [24.7%] Week 16 Bacteroidetes; Bacteroidales Axis.1 [80.8%] Axis.1 [65.4%] Axis.1 [49.6%] Actinobacteria; Bifidobacterium Week 16 Week 20 Week 24 Week 20 p=0.339 p=0.036 p=0.021 Firmicutes; Dehalobacterium
    [Show full text]
  • A Review of Ureaplasma Diversum: a Representative of the Mollicute Class Associated with Reproductive and Respiratory Disorders in Cattle
    REVIEW published: 18 February 2021 doi: 10.3389/fvets.2021.572171 A Review of Ureaplasma diversum: A Representative of the Mollicute Class Associated With Reproductive and Respiratory Disorders in Cattle Manoel Neres Santos Junior 1,2, Nayara Silva de Macêdo Neres 1, Guilherme Barreto Campos 1, Bruno Lopes Bastos 1, Jorge Timenetsky 3 and Lucas Miranda Marques 1,2,3* 1 Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil, 2 Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil, 3 Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil The Mollicutes class encompasses wall-less microbes with a reduced genome. They may infect plants, insects, humans, and animals including those on farms and in livestock. Edited by: Ureaplasma diversum is a mollicute associated with decreased reproduction mainly in the Michael Kogut, conception rate in cattle, as well as weight loss and decreased quality in milk production. United States Department of Agriculture, United States Therefore, U. diversum infection contributes to important economic losses, mainly in Reviewed by: large cattle-producing countries such as the United States, China, Brazil, and India. Marie Rene Culhane, The characteristics of Mollicutes, virulence, and pathogenic variations make it difficult to University of Minnesota, United States control their infections. Genomic analysis, prevalence studies, and immunomodulation Christine Letitia
    [Show full text]
  • Phylogenomics of Expanding Uncultured Environmental Tenericutes
    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.21.914887; this version posted January 23, 2020. 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-ND 4.0 International license. 1 Phylogenomics of expanding uncultured environmental Tenericutes 2 provides insights into their pathogenicity and evolutionary 3 relationship with Bacilli 4 Yong Wang1,*, Jiao-Mei Huang1,2, Ying-Li Zhou1,2, Alexandre Almeida3,4, Robert D. 5 Finn3, Antoine Danchin5,6, Li-Sheng He1 6 1Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 7 Hai Nan, China 8 2 University of Chinese Academy of Sciences, Beijing, China 9 3European Molecular Biology Laboratory, European Bioinformatics Institute 10 (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 11 4Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK. 12 5Department of Infection, Immunity and Inflammation, Institut Cochin INSERM 13 U1016 - CNRS UMR8104 - Université Paris Descartes, 24 rue du Faubourg 14 Saint-Jacques, 75014 Paris, France 15 6School of Biomedical Sciences, Li Kashing Faculty of Medicine, University of Hong 16 Kong, 21 Sassoon Road, SAR Hong Kong, China 17 18 *Corresponding author: 19 Yong Wang, PhD 20 Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences 21 No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. of China 22 Phone: 086-898-88381062 23 E-mail: [email protected] 24 Running title: Genomics of environmental Tenericutes 25 Keywords: Bacilli; autotrophy; pathogen; gut microbiome; environmental 26 Tenericutes 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.21.914887; this version posted January 23, 2020.
    [Show full text]
  • Gut Microbiota of Tenebrio Molitor and Their Response to Environmental Change Jaejoon Jung1,2, Aram Heo1, Yong Woo Park1, Ye Ji Kim1, Hyelim Koh1, and Woojun Park1*
    J. Microbiol. Biotechnol. (2014), 24(7), 888–897 http://dx.doi.org/10.4014/jmb.1405.05016 Research Article Review jmb Gut Microbiota of Tenebrio molitor and Their Response to Environmental Change Jaejoon Jung1,2, Aram Heo1, Yong Woo Park1, Ye Ji Kim1, Hyelim Koh1, and Woojun Park1* 1Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea 2Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea Received: May 8, 2014 Revised: May 23, 2014 A bacterial community analysis of the gut of Tenebrio molitor larvae was performed using Accepted: May 26, 2014 pyrosequencing of the 16S rRNA gene. A predominance of genus Spiroplasma species in phylum Tenericutes was observed in the gut samples, but there was variation found in the community composition between T. molitor individuals. The gut bacteria community structure First published online was not significantly affected by the presence of antibiotics or by the exposure of T. molitor May 27, 2014 larvae to a highly diverse soil bacteria community. A negative relationship was identified *Corresponding author between bacterial diversity and ampicillin concentration; however, no negative relationship Phone: +82-2-3290-3067; was identified with the addition of kanamycin. Ampicillin treatment resulted in a reduction in Fax: +82-2-953-0737; the bacterial community size, estimated using the 16S rRNA gene copy number. A detailed E-mail: [email protected] phylogenetic analysis indicated that the Spiroplasma-associated sequences originating from the T. molitor larvae were distinct from previously identified Spiroplasma type species, implying the presence of novel Spiroplasma species.
    [Show full text]
  • A Metagenomics Roadmap to the Uncultured Genome Diversity in Hypersaline Soda Lake Sediments Charlotte D
    Vavourakis et al. Microbiome (2018) 6:168 https://doi.org/10.1186/s40168-018-0548-7 RESEARCH Open Access A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments Charlotte D. Vavourakis1 , Adrian-Stefan Andrei2†, Maliheh Mehrshad2†, Rohit Ghai2, Dimitry Y. Sorokin3,4 and Gerard Muyzer1* Abstract Background: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages. Results: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L−1. The recovered 16S rRNA gene sequences were mostly from Bacteria,evenin the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.
    [Show full text]