DOCSLIB.ORG

Cell-To-Cell Bacterial Interactions Promoted by Drier Conditions on Soil Surfaces

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Cell-To-Cell Bacterial Interactions Promoted by Drier Conditions on Soil Surfaces Cell-to-cell bacterial interactions promoted by drier conditions on soil surfaces Robin Tecona,1, Ali Ebrahimia,2, Hannah Kleyera, Shai Erev Levia, and Dani Ora aSoil & Terrestrial Environmental Physics, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, 8092 Zürich, Switzerland Edited by Steven E. Lindow, University of California, Berkeley, CA, and approved August 13, 2018 (received for review May 15, 2018) Bacterial cell-to-cell interactions are in the core of evolutionary and 100 cells within a radius of 20 μm). For certain high cell density ecological processes in soil and other environments. Under most “hotspots,” e.g., in the rhizosphere (19), the number of neighbors conditions, natural soils are unsaturated where the fragmented can increase significantly. Although the distance to the nearest aqueous habitats and thin liquid films confine bacterial cells within neighboring cell can be relatively small on average (∼10 μmin small volumes and close proximity for prolonged periods. We report densely populated topsoils), it is highly spatially variable, and, effects of a range of hydration conditions on bacterial cell-level since soil bacterial distributions show a high degree of clustering, interactions that are marked by plasmid transfer between donor colonized microsites are often spatially isolated (19). To sum up, and recipient cells within populations of the soil bacterium Pseudo- the level of bacterial cell-to-cell interactions in soil may be far monas putida. Using hydration-controlled sand microcosms, we more limited than would appear from the high cell density values 9– 10 · −1 demonstrate that the frequency of cell-to-cell contacts under pre- commonly reported (10 10 cells g ) (20) due to the high scribed hydration increases with lowering water potential values surface area per volume of soil and the clustered spatial distri- (i.e., under drier conditions where the aqueous phase shrinks and bution of soil bacteria. In this background of limited opportu- nities for cell-to-cell interactions, additional environmental fragments). These observations were supported using a mechanistic factors regulate the frequency and duration of cell-to-cell en- individual-based model for linking macroscopic soil water potential counters in soil. Developing a better mechanistic understanding to microscopic distribution of liquid phase and explicit bacterial cell of how key factors affect encounters among bacterial cells is interactions in a simplified porous medium. Model results are in important for revealing basic principles that govern soil micro- good agreement with observations and inspire confidence in the bial community diversity, dynamics, and functioning. underlying mechanisms. The study highlights important physical In this study, we hypothesize that the probability of bacterial factors that control short-range bacterial cell interactions in soil cell-to-cell encounters and interactions on hydrated rough sur- and on surfaces, specifically, the central role of the aqueous phase faces such as found in soil is modified by soil properties and in mediating bacterial interactions and conditions that promote ge- hydration conditions. We thus seek to link macroscopic variables netic information transfer in support of soil microbial diversity. such as the soil water potential, soil pore spaces, and internal surface area to biological interactions that take place in aqueous conjugation | soil physics | vadose zone | Pseudomonas putida | HGT microhabitats. Specifically, we propose that cell-to-cell bacterial acterial cell-to-cell interactions sustain key evolutionary and Significance Becological processes in all environments, including horizon- tal gene transfer mediated by conjugative pili (1, 2), nutrient Despite a high number of microbial cells and species present in cross-feeding (e.g., in syntrophy; ref. 3), and chemical signaling small volumes of soil, detailed observations suggest that most that shapes social behaviors (4). To interact, microorganisms bacteria interact with only a few other individuals. These inter- have to remain in direct physical contact or within a range per- actions between cells are crucial to many soil processes including mitting effective molecular exchanges by diffusion, i.e., most imparting genetic traits (e.g., antibiotic resistance) and microbial MICROBIOLOGY interactions occur at the scale of individual microbes (5). Ulti- evolution, yet our understanding of the controlling environmental mately, cumulative cell-to-cell exchanges determine the overall factors remains sketchy. Based on evidence from experiments in bacterial activity in a given habitat, affecting large-scale fluxes soil microcosms and results of a mathematical model, we dem- and, hence, impacting global ecosystem processes (6). onstrate that a ubiquitous physical factor such as fragmentation Bacteria that inhabit natural porous media such as soil expe- of the aqueous phase commonly found in unsaturated soils af- rience life in a complex 3D pore network and on rough surface fects the ranges and frequency of cell-to-cell bacterial interactions. architecture, with heterogeneous nutrient resources and frag- Our findings thus help reveal some of the basic principles that mented aqueous niches that limit their distribution, dispersion, control microbial life and diversity in soil environments. and contact with neighbors, but can locally increase cell density and proximity (7–11). Evidence suggests that (i) the distribution Author contributions: R.T., A.E., H.K., S.E.L., and D.O. designed research; A.E. designed the of microorganisms in soil is highly patchy, with nonrandom mi- mathematical model; R.T., A.E., H.K., and S.E.L. performed research; R.T., A.E., H.K., and crohabitats colonized by single cells or microcolonies (12–15), S.E.L. analyzed data; and R.T., A.E., and D.O. wrote the paper. and that (ii) although soil microbial density is high in comparison The authors declare no conflict of interest. with other habitats, cells occupy no more than a few percent of This article is a PNAS Direct Submission. the pore spaces of an average soil and only a small fraction Published under the PNAS license. < ( 1%) of the available soil surfaces (9, 16, 17). This spatial Data deposition: The Modeling data and code have been deposited in the ETH Research context—together with microbial growth and motility (18)— Collection, https://www.research-collection.ethz.ch/handle/20.500.11850/284650 (DOI: 10. controls the probability for a bacterial cell to encounter another 3929/ethz-b-000284650). cell, and therefore to interact, in soil. Based on a detailed 1To whom correspondence should be addressed. Email: [email protected]. analysis of bacterial distributions in hundreds of soil thin sections 2Present address: Ralph M. Parsons Laboratory for Environmental Science and Engineer- and on statistical modeling, Raynaud and Nunan (19) have ing, Department of Civil and Environmental Engineering, Massachusetts Institute of concluded that the potential for cell-to-cell interactions in soil is Technology, Cambridge, MA 02139. relatively limited, both in terms of the number of interacting cells This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. and of the number of different species to interact with. The vi- 1073/pnas.1808274115/-/DCSupplemental. cinity of a soil bacterium typically harbors few neighbors (10 to Published online September 12, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1808274115 PNAS | September 25, 2018 | vol. 115 | no. 39 | 9791–9796 Downloaded by guest on September 29, 2021 interactions could be promoted under hydration conditions that locally increase the likelihood and duration of cell encounters while limiting cell dispersal. To systematically investigate this question, we have used the exchange of a conjugative plasmid as a proxy for close encounters between bacterial cells, with the soil bacterium Pseudomonas putida (21) selected as a donor and recipient of a broad-host range plasmid isolated from soil envi- ronments (Fig. 1). Sand microcosms were used as simple and well-defined porous environments for assessing conjugation events as function of hydration conditions, as determined by a prescribed matric potential (Fig. 2 and SI Appendix, Supple- mentary Methods for details). In unsaturated soil, the matric potential results from capillary and adsorptive interactions that retain water in pores and within roughness elements (22, 23). The matric potential is often expressed as a negative pressure (relative to atmospheric pressure): where zero value marks complete water Fig. 2. Sand microcosms with controlled hydration conditions. (A) Photo- saturation, while progressively negative values correspond to drier graph shows an assembled system, with microcosms connected to a liquid conditions (22, 23). We use the simple experimental system (Figs. medium reservoir (0.1× TSB). The height of the liquid column (h) prescribes a 1 and 2) to directly study the relation between a biological cell-to- fixed suction to the sand phase via the ceramic plate, which mimics the ef- cell interaction (bacterial conjugation) and a physical parameter fects of matric potential in porous media (e.g., h = 10-cm produces a water (matric potential) relevant to soil. In addition to experiments, matric potential of ∼−1 kPa). Inset shows stereomicroscope image of the mathematical modeling provides a means for generalization and quartz sand layer. (B) Illustration of the microcosm unit,
Load more

Recommended publications
  • Comprehensive Analysis of Mobile Genetic Elements in the Gut Microbiome Reveals Phylum-Level Niche-Adaptive Gene Pools
    bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. 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 Comprehensive analysis of mobile genetic elements in the gut microbiome 2 reveals phylum-level niche-adaptive gene pools 3 Xiaofang Jiang1,2,†, Andrew Brantley Hall2,3,†, Ramnik J. Xavier1,2,3,4, and Eric Alm1,2,5,* 4 1 Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, 5 Cambridge, MA 02139, USA 6 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 7 3 Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard 8 Medical School, Boston, MA 02114, USA 9 4 Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General 10 Hospital and Harvard Medical School, Boston, MA 02114, USA 11 5 MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 12 02142, USA 13 † Co-first Authors 14 * Corresponding Author bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. 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. 15 Abstract 16 Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer 17 could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could 18 threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological 19 importance and medical relevance, MGEs from the gut microbiome have not been systematically 20 characterized.
    [Show full text]
  • Section 4. Guidance Document on Horizontal Gene Transfer Between Bacteria
    306 - PART 2. DOCUMENTS ON MICRO-ORGANISMS Section 4. Guidance document on horizontal gene transfer between bacteria 1. Introduction Horizontal gene transfer (HGT) 1 refers to the stable transfer of genetic material from one organism to another without reproduction. The significance of horizontal gene transfer was first recognised when evidence was found for ‘infectious heredity’ of multiple antibiotic resistance to pathogens (Watanabe, 1963). The assumed importance of HGT has changed several times (Doolittle et al., 2003) but there is general agreement now that HGT is a major, if not the dominant, force in bacterial evolution. Massive gene exchanges in completely sequenced genomes were discovered by deviant composition, anomalous phylogenetic distribution, great similarity of genes from distantly related species, and incongruent phylogenetic trees (Ochman et al., 2000; Koonin et al., 2001; Jain et al., 2002; Doolittle et al., 2003; Kurland et al., 2003; Philippe and Douady, 2003). There is also much evidence now for HGT by mobile genetic elements (MGEs) being an ongoing process that plays a primary role in the ecological adaptation of prokaryotes. Well documented is the example of the dissemination of antibiotic resistance genes by HGT that allowed bacterial populations to rapidly adapt to a strong selective pressure by agronomically and medically used antibiotics (Tschäpe, 1994; Witte, 1998; Mazel and Davies, 1999). MGEs shape bacterial genomes, promote intra-species variability and distribute genes between distantly related bacterial genera. Horizontal gene transfer (HGT) between bacteria is driven by three major processes: transformation (the uptake of free DNA), transduction (gene transfer mediated by bacteriophages) and conjugation (gene transfer by means of plasmids or conjugative and integrated elements).
    [Show full text]
  • The Obscure World of Integrative and Mobilizable Elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget
    The obscure world of integrative and mobilizable elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget To cite this version: Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget. The obscure world of integrative and mobilizable elements: Highly widespread elements that pirate bacterial conjugative systems. Genes, MDPI, 2017, 8 (11), pp.337. 10.3390/genes8110337. hal- 01686871 HAL Id: hal-01686871 https://hal.archives-ouvertes.fr/hal-01686871 Submitted on 26 May 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. Distributed under a Creative Commons Attribution| 4.0 International License G C A T T A C G G C A T genes Review The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems Gérard Guédon *, Virginie Libante, Charles Coluzzi, Sophie Payot and Nathalie Leblond-Bourget * ID DynAMic, Université de Lorraine, INRA, 54506 Vandœuvre-lès-Nancy, France; [email protected] (V.L.); [email protected] (C.C.); [email protected] (S.P.) * Correspondence: [email protected] (G.G.); [email protected] (N.L.-B.); Tel.: +33-037-274-5142 (G.G.); +33-037-274-5146 (N.L.-B.) Received: 12 October 2017; Accepted: 15 November 2017; Published: 22 November 2017 Abstract: Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements.
    [Show full text]
  • Genetic Exchange in Bacteria
    Systems Microbiology Monday Oct 16 - Ch 10 -Brock Genetic Exchange in Bacteria •• HomologousHomologous recombinationrecombination •• TransformationTransformation •• PlasmidsPlasmids andand conjugationconjugation •• TransposableTransposable elementselements •• TransductionTransduction (virus(virus mediatedmediated xchangexchange)) Gene exchange in bacteria • Transfer of DNA from one bacterium to another is a common means of gene dispersal. It has a big effect on bacterial evolution, and tremendous practical implications. For example, lateral transfer is responsible for the spread drug resistance determinants between bacterial species. • Three common mechanisms of lateral gene exchange : – Transformation (extracellular DNA uptake) – Conjugation (bacterial mating systems) – Transduction (viral mediated gene exchange) RecA mediated Homologous recombination Images removed due to copyright restrictions. See Figures 10-9 and 10-10 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms.11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291. Gene exchange in bacteriaTransformation The Griffith Experiment S Injection Dead mouse; • Discovered by Griffith in yields S1 cells 1928 during the course of his Live "smooth" (encapsulated) studies of virulence in type 1 pneumococci (S1) Streptococcus pneumoniae. Dead S Live mouse Heat-killed S1 • S=smooth colony Live mouse morphotype Live "rough" (unencapsulated) pneumococci (R1 or R2) derived by subculture from S1 or S2, respectively • R=rough colony Dead mouse; yields S cells morphotype R1 + Dead S + 1 Live R1 Killed S1 R2 + Dead S + Dead mouse; yields S1 cells Live R2 Killed S2 Figure by MIT OCW. Gene exchange mechanisms in bacteria Transformation The Griffith Experiment Injection Dead mouse; S yields S cells Avery, MacLeod, and McCarthy (1944) 1 fractionation studies led to conclusion that Live "smooth" (encapsulated) type 1 pneumococci (S ) transformation principle is DNA.
    [Show full text]
  • Lab Exercise 15: Bacterial Conjugation
    Microbiology BIOL 275 BACTERIAL CONJUGATION I. OBJECTIVES • To demonstrate the technical procedure to monitor the conjugational transfer of genetic material from one cell to another. • To learn about the various genetic elements involved in bacterial sex and recombination events. • To recognize and discuss the advantages and limitations of the conjugational procedure in genetic recombination experiments. II. INTRODUCTION There are three different mechanisms for genetic exchange between bacteria: conjugation, transformation and transduction. Conjugation has been shown to occur in many bacterial species especially the Gram negative organisms. In Enterobacteriaceae (Escherichia, Salmonella, Shigella, Vibrio, etc.), the transfer has been shown to cross the taxonomic lines with varying rates of efficiency. Thus, conjugation has become a tool to study the location and function of many genes, including genes responsible for virulence, antibiotic resistance, metabolic functions, regulatory proteins, phage attachment sites, etc. E. coli has been the model organism in conjugation studies. It may become infected with an extrachromosomal genetic element (a plasmid called the F factor) which mediates certain events such as the synthesis of a pilus (the F or sex pilus), and the rapid infection of all susceptible bacteria with this F factor. The pilus has been shown to facilitate attachment of the male (or F+ cells) to the female (or F- cells) which do not contain the F factor. It was previously thought that the hollow center of the pilus constituted a passageway for the F factor to be transferred to the female. However, recent evidence suggests that the pilus may be used as a "hook" to bring the two cells close together and that the DNA transfer actually occurs outside the pilus.
    [Show full text]
  • Bacterial Conjugation
    16 Mechanisms of Genetic Variation 1 16.1 Mutations 1. Distinguish spontaneous from induced mutations, and list the most common ways each arises 2. Construct a table, concept map, or picture to summarize how base analogues, DNA-modifying agents, and intercalating agents cause mutations 3. Discuss the possible effects of mutations 2 Mutations: Their Chemical Basis and Effects • Stable, heritable changes in sequence of bases in DNA – point mutations most common • from alteration of single pairs of nucleotide • from the addition or deletion of nucleotide pairs – larger mutations are less common • insertions, deletions, inversions, duplication, and translocations of nucleotide sequences • Mutations can be spontaneous or induced 3 16.4 Creating Additional Genetic Variability 1. Describe in general terms how recombinant eukaryotic organisms arise 2. Distinguish vertical gene transfer from horizontal gene transfer 3. Summarize the four possible outcomes of horizontal gene transfer 4. Compare and contrast homologous recombination and site-specific recombination 4 Creating Additional Genetic Variability • Mutations are subject to selective pressure – each mutant form that survives becomes an allele, an alternate form of a gene • Recombination is the process in which one or more nucleic acids are rearranged or combined to produce a new nucleotide sequence (recombinants) 5 Sexual Reproduction and Genetic Variability • Vertical gene transfer = transfer of genes from parents to progeny • In eukaryotes – sexual reproduction is accompanied by genetic
    [Show full text]
  • Mechanism of Genetic Recombination During Bacterial Conjugation of Escherzchza Coli K-12
    MECHANISM OF GENETIC RECOMBINATION DURING BACTERIAL CONJUGATION OF ESCHERZCHZA COLI K-12. 11. INCORPORATION OF THE DONOR DNA FRAGMENT INTO THE RECOMBINANT CHROMOSOME S. E. BRESLER AND V. A. LANZOV Institute of High Molecular Weight Compounds, Academy of Sciences of USSR, Leningrad Received November 30, 1966 INVESTIGATION of genetic recombination in bacteriophages and bacteria (KELLENBERGER.ZICHICHI and WEIGLE1961 ; MESELSONand WEIGLE1961 ; BODMERand GANESAN1964; FOXand ALLEN1965; OPPENHEIMand RILEY1966) has already shown that of the two recombination mechanisms, ILcopychoice” and “breakage-reunion”, the latter is the more plausible. Nevertheless, the model of “copy choice” acquired wide popularity. Therefore it is important to perform new experiments giving direct proofs of physical integration of parental material into recombinants. One experiment of this type fulfilled with a conjugation system is that of SIDDIQI( 1963). Using radioactively labeled F- cells and selecting true recombi- nants (according to a recessive marker T6‘) SIDDIQIsucceeded in demonstrating that the main part of the recipient cell genome (+ 80%) is inherited by the recombinant. Our aim was to design a complementary experiment to show that a part of the labeled donor genome can be detected in the cells which are true recombinants after conjugation. Since it was expected that the recombinant inherits only a small fragment of the donor DNA, the method has to be sufficiently sensitive. The experimental system satisfying these conditions is as follows: 1. The experiment is performed using a population of mainly mononuclear E. coti cells. The possibility of obtaining such a population was shown in the papers of WITKIN( 1951) and MCFALL,PARDEE and STENT(1958). 2.
    [Show full text]
  • Bacteria Evolving: Tracing the Origins of a MRSA Epidemic
    STUDENT VERSION Bacteria Evolving: Tracing the Origins of a MRSA Epidemic PASSAGE TWO How Did MRSA Evolve? def initions DNA: Deoxyribonucleic What allowed USA300 to thrive outside a hospital set- acid is the organic ting, and with such virulence? Scientists knew the answer molecule that forms the genetic material of an lay in the bacteria’s genome, the sum of all its genetic organism. Chromosomes material. Within the bacteria’s genome were the clues are made of DNA. that could explain how the USA300 strain of MRSA had evolved. gene: a section of DNA on a chromosome that Different Types of Mutations encodes, individually Like all organisms, bacteria can acquire new traits through or as part of a group mutations. Mutations are any change in the sequence of of genes, for a specific DNA nucleotides within an organism’s genome. The main hereditary trait. cause of mutations are exposure to foreign chemicals or genome: the complete radiation, errors during DNA replication, and from inser- genetic material or base tion or deletion of DNA segments. If a mutation is benefi- sequence of an organism cial, it gives the organism an evolutionary advantage by or species. helping it and its descendants to survive in a new envi- genotype: the genetic ronment. This is the process of natural selection. makeup of an individual These types of mutations can happen in any organism. In or species. bacteria, DNA can also be acquired through the process phenotype: the of DNA transfer. That means that bacteria can get whole observable characteristics new sets of DNA from other bacteria, creating sudden of an organism or species, and dramatic changes in their genome.
    [Show full text]
  • A First Approach to Individual-Based Modeling of the Bacterial Conjugation Dynamics
    Facultad Informatica´ Universidad Politecnica´ de Madrid TESIS DE MASTER´ Master´ de Investigacion´ en Tecnolog´ıas para el Desarrollo de Sistemas Software Complejos A first approach to individual-based modeling of the bacterial conjugation dynamics Autor: Antonio P. Garc´ıa Tutor: Alfonso Rodr´ıguez-Paton´ Aradas Septiembre, 2011 FACULTAD DE INFORMÁTICA PRESENTACIÓN DE TESIS DE MÁSTER Alumno: Máster: Título de la Tesis: Tutor: VºBº del Tutor, El alumno, Fecha: A` minha av´o,Dora que se foi este ano. Resumen El objetivo fundamental de esta tesis es emplear el modelado basado en individuos pa- ra el estudio de la din´amica de invasi´onde los pl´asmidosconjugativos en poblaciones bacterianas sobre superficies s´olidas.Los pl´asmidosson peque~nossegmentos de ADN, normalmente circulares que poseen su propio mecanismo de replicaci´on,independiente del ADN cromos´omicoprincipal de las c´elulasbacterianas y que sobreviven como par´asi- tos utilizando la maquinaria celular de su hospedero en su propio beneficio. Adem´asde la capacidad de replicaci´onlos pl´asmidosson capaces de auto-transferirse a otras c´elulas bacterianas en un proceso conocido como conjugaci´onbacteriana. La persistencia como elemento gen´eticom´ovilde los pl´asmidosen escala evolutiva no est´acompletamente ca- racterizada, puesto que en muchas situaciones donde no exista una presi´onselectiva que favorezca las c´elulasportadoras del pl´asmido,el coste metab´olicoque representa deber´ıa paulatinamente eliminarlos de la poblaci´on.Empleando un modelo basado en la ley de acci´onde masas[SL77] se postula que las condiciones requeridas para que un pl´asmido conjugativo se mantenga de forma estable en una poblaci´onson bastante amplias, siendo suficiente que la cantidad de c´elulasinfectadas inicialmente, sea elevada para compensar la p´erdidasegregativa y el coste metab´olicoque acarrea el hecho de portar el pl´asmi- do.
    [Show full text]
  • Genetic Cargo and Bacterial Species Set the Rate of Vesicle-Mediated Horizontal Gene Transfer Received: 31 March 2017 Frances Tran1 & James Q
    www.nature.com/scientificreports OPEN Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer Received: 31 March 2017 Frances Tran1 & James Q. Boedicker1,2 Accepted: 27 June 2017 Most bacteria release extracellular vesicles (EVs). Recent studies have found these vesicles are Published: xx xx xxxx capable of gene delivery, however the consequences of vesicle-mediated transfer on the patterns and rates of gene fow within microbial communities remains unclear. Previous studies have not determined the impact of both the genetic cargo and the donor and recipient species on the rate of vesicle-mediated gene exchange. This report examines the potential for EVs as a mechanism of gene transfer within heterogeneous microbial populations. EVs were harvested from three species of Gram- negative microbes carrying diferent plasmids. The dynamics of gene transfer into recipient species was measured. This study demonstrates that vesicles enable gene exchange between fve species of Gram-negative bacteria, and that the identity of the genetic cargo, donor strain, and recipient strain all infuence gene transfer rates. Each species released and acquired vesicles containing genetic material to a variable degree, and the transfer rate did not correlate with the relatedness of the donor and recipient species. The results suggest that EVs may be a general mechanism to exchange non-specialized genetic cargo between bacterial species. Microorganisms possess complex abilities to transfer genetic material through horizontal gene transfer (HGT), fundamentally shaping genetic landscapes and afecting biological functions1–4. Te capacity for DNA exchange in bacteria and the plasticity of their genetic material has amplifed the rate of adaptation and evolu- tion across species and has allowed for stability and growth of complex microbial ecosystems in a multitude of environments5–8.
    [Show full text]
  • Bacterial Conjugation and Its Inhibition
    Bacterial Conjugation and its Inhibition: The Hows and Whys of Conjugation and What Can be Done to Control It Scott A. Lujan A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the department of Biochemistry and Biophysics. Chapel Hill, NC 2008 Approved by Professor Matthew Redinbo, Ph.D. Professor Richard Wolfenden, Ph.D. Professor Steve Matson, Ph.D. Professor Gary Pielak, Ph.D. Professor Brenda Temple, Ph.D. © 2008 Scott A. Lujan ALL RIGHTS RESERVED ii Abstract SCOTT A. LUJAN: Bacterial Conjugation and its Inhibition: The Hows and Whys of Conjugation and What Can be Done to Control It (Under the direction of Matthew R. Redinbo, Ph.D.) Conjugation is the primary vehicle for the horizontal transfer virulence factor genes, such as antibiotic resistance, within and between bacterial strains. In certain epicenters, such as hospitals in less developed parts of the world, immune-compromised patients and misuse of antibiotics combine to select for the development and dissemination of these pathogenicity factors via conjugation. Inhibition of conjugation would prove a boon for curbing the creation and spread of new virulent or multi-drug resistant strains. DNA relaxases are the keystone proteins of each conjugative system. TraI is the relaxase of the F plasmid, the archetypal model system for conjugation. Toward revelation and inhibition of relaxase mechanisms, I used bioinformatics and limited proteolysis to find and identify new domains on the F TraI enzyme. I then solved TraI/DNA co-crystal structures that showed a novel DNA binding mode.
    [Show full text]
  • Integrative and Conjugative Elements (ICE) and Associated Cargo Genes Within and Across Hundreds of Bacterial Genera
    bioRxiv preprint doi: https://doi.org/10.1101/2020.04.07.030320; this version posted April 9, 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. Journal of XYZ, 20xx, 1–21 doi: xx.xxxx/xxxx Manuscript in Preparation Paper P APER Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera J. H. Kaufman1,*, I. Terrizzano1,*, G. Nayar1,*, E. Seabolt1,*, A. Agarwal1,*, I. B. Slizovskiy2,† and N. R. Noyes2,† 1IBM Research - Almaden, 650 Harry Rd., San Jose, CA 95120-6099 and 2Department of Veterinary Population Medicine, University of Minnesota, 1988 Fitch Ave, St. Paul, MN 55108 *[email protected], [email protected], [email protected], [email protected], [email protected] †[email protected] Abstract Horizontal gene transfer mediated by integrative and conjugative elements (ICE) is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The rate of ICE-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. In this paper we report a big data analysis of ICE and associated cargo genes across over 200,000 bacterial genomes representing 1,345 genera. Our results reveal that half of bacterial genomes contain one or more known ICE features ("ICE genomes"), and that the associated genetic cargo may play an important role in the spread of AMR genes within and between bacterial genera.
    [Show full text]